channotation / chap Goto Github PK
View Code? Open in Web Editor NEWCHAP is a tool for the functional annotation of ion channel structures:
Home Page: http://www.channotation.org
License: Other
CHAP is a tool for the functional annotation of ion channel structures:
Home Page: http://www.channotation.org
License: Other
cmak .. run ok however when i run make i got the following error. i will appreciate any help.
[ 6%] Built target googletest
[ 7%] Building CXX object CMakeFiles/chap.dir/src/aggregation/number_density_calculator.cpp.o
In file included from /usr/local/gromacs/include/gromacs/math/vec.h:111:0,
from /home/afa32/local/chap-version_0_9_1/include/geometry/spline_curve_1D.hpp:33,
from /home/afa32/local/chap-version_0_9_1/include/aggregation/number_density_calculator.hpp:32,
from /home/afa32/local/chap-version_0_9_1/src/aggregation/number_density_calculator.cpp:29:
/usr/local/gromacs/include/gromacs/math/vectypes.h:96:41: error: ‘remove_cv_t’ is not a member of ‘std’
static_assert(!std::is_pointer<std::remove_cv_t>::value,
^~~~~~~~~~~
/usr/local/gromacs/include/gromacs/math/vectypes.h:96:41: note: suggested alternative: ‘remove_cv’
static_assert(!std::is_pointer<std::remove_cv_t>::value,
^~~~~~~~~~~
remove_cv
/usr/local/gromacs/include/gromacs/math/vectypes.h:96:41: error: ‘remove_cv_t’ is not a member of ‘std’
/usr/local/gromacs/include/gromacs/math/vectypes.h:96:41: note: suggested alternative: ‘remove_cv’
static_assert(!std::is_pointer<std::remove_cv_t>::value,
^~~~~~~~~~~
remove_cv
/usr/local/gromacs/include/gromacs/math/vectypes.h:96:53: error: template argument 1 is invalid
static_assert(!std::is_pointer<std::remove_cv_t>::value,
^~~~~~~~~
/usr/local/gromacs/include/gromacs/math/vectypes.h:96:66: error: ‘::value’ has not been declared
static_assert(!std::is_pointer<std::remove_cv_t>::value,
^~~~~
/usr/local/gromacs/include/gromacs/math/vectypes.h:96:66: note: suggested alternative: ‘valloc’
static_assert(!std::is_pointer<std::remove_cv_t>::value,
^~~~~
valloc
In file included from /home/afa32/local/chap-version_0_9_1/include/geometry/spline_curve_1D.hpp:33:0,
from /home/afa32/local/chap-version_0_9_1/include/aggregation/number_density_calculator.hpp:32,
from /home/afa32/local/chap-version_0_9_1/src/aggregation/number_density_calculator.cpp:29:
/usr/local/gromacs/include/gromacs/math/vec.h:630:6: error: ‘remove_const_t’ in namespace ‘std’ does not name a template type
std::remove_const_t norm(T* v)
^~~~~~~~~~~~~~
/usr/local/gromacs/include/gromacs/math/vec.h:635:6: error: ‘remove_const_t’ in namespace ‘std’ does not name a template type
std::remove_const_t norm2(T* v)
^~~~~~~~~~~~~~
CMakeFiles/chap.dir/build.make:107: recipe for target 'CMakeFiles/chap.dir/src/aggregation/number_density_calculator.cpp.o' failed
make[2]: *** [CMakeFiles/chap.dir/src/aggregation/number_density_calculator.cpp.o] Error 1
CMakeFiles/Makefile2:388: recipe for target 'CMakeFiles/chap.dir/all' failed
make[1]: *** [CMakeFiles/chap.dir/all] Error 2
Makefile:159: recipe for target 'all' failed
make: *** [all] Error 2
Hi everyone!
I am having some trouble at the cmake step, during the compilation
Here I attach the output. Gromacs 2020 is installed in /usr/local/gromacs
Thanks in advance!
Gera!
`cmake ..
-- The CXX compiler identification is GNU 7.5.0
-- The C compiler identification is GNU 7.5.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Boost version: 1.65.1
-- Found LAPACKE: /usr/include/x86_64-linux-gnu
-- Found GROMACS: 2020.2
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
CMake Error at CMakeLists.txt:155 (add_executable):
Target "chap" links to target "OpenMP::OpenMP_CXX" but the target was not
found. Perhaps a find_package() call is missing for an IMPORTED target, or
an ALIAS target is missing?
CMake Error at test/CMakeLists.txt:42 (add_executable):
Target "runAllTests" links to target "OpenMP::OpenMP_CXX" but the target
was not found. Perhaps a find_package() call is missing for an IMPORTED
target, or an ALIAS target is missing?
CMake Error in CMakeLists.txt:
Imported target "libgromacs" includes non-existent path
"/usr/local/gromacs/COMPONENT"
in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:
The path was deleted, renamed, or moved to another location.
An install or uninstall procedure did not complete successfully.
The installation package was faulty and references files it does not
provide.
CMake Error in CMakeLists.txt:
Imported target "libgromacs" includes non-existent path
"/usr/local/gromacs/COMPONENT"
in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:
The path was deleted, renamed, or moved to another location.
An install or uninstall procedure did not complete successfully.
The installation package was faulty and references files it does not
provide.
CMake Error in test/CMakeLists.txt:
Imported target "libgromacs" includes non-existent path
"/usr/local/gromacs/COMPONENT"
in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:
The path was deleted, renamed, or moved to another location.
An install or uninstall procedure did not complete successfully.
The installation package was faulty and references files it does not
provide.
CMake Error in test/CMakeLists.txt:
Imported target "libgromacs" includes non-existent path
"/usr/local/gromacs/COMPONENT"
in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:
The path was deleted, renamed, or moved to another location.
An install or uninstall procedure did not complete successfully.
The installation package was faulty and references files it does not
provide.
-- Generating done
-- Build files have been written to: /home/geraz/chap-version_0_9_1/build`
Hello,
I am having some problems installing chap. I have installed the proper libraries and when I do cmake, there is no problem:
-- The CXX compiler identification is GNU 5.5.0
-- The C compiler identification is GNU 5.5.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Boost version: 1.65.1
-- Found LAPACKE: /usr/include/x86_64-linux-gnu
-- Found GROMACS: 2016.3
CMake Warning at /usr/local/gromacs/share/cmake/gromacs/gromacs-config.cmake:125 (message):
You are compiling with a different C++ compiler from the one that was used
to compile GROMACS. This may lead to linking or runtime problems. GROMACS
was compiled with GNU 5.4.0 (/usr/bin/g++-5).
Call Stack (most recent call first):
CMakeLists.txt:87 (gromacs_check_compiler)
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
-- Generating done
-- Build files have been written to: /data/sperez/bin2/chap-version_0_9_1/build
But when I compile I get:
make[2]: *** No rule to make target '/home/oliverfl/anaconda2/envs/py2/lib/libz.so', needed by 'chap'. Stop.
CMakeFiles/Makefile2:355: recipe for target 'CMakeFiles/chap.dir/all' failed
make[1]: *** [CMakeFiles/chap.dir/all] Error 2
Makefile:140: recipe for target 'all' failed
make: *** [all] Error 2
This library is an old installation of anaconda that is now removed, but it still finds it. I have checked in my environment variables (using env) and it is not in the environment varibles.
Could you help me?
Thank you very much in advanced,
Best,
Sergio
Hi, I am trying to use CHAP with singularity image. But it give the following error. I am using singularity image with Mac, uisng SingularityCE vagrant box with ubuntu 18.04, singularity version 3.8.1.
singularity shell --nv chap_singularity_version2.simg
INFO: Could not find any nv files on this host!
WARNING: Could not find any nv libraries on this host!
WARNING: You may need to manually edit /usr/local/etc/singularity/nvliblist.conf
FATAL: could not open image /home/vagrant/chap_singularity_version2.simg: image format not recognized
Hi Inniag,
As I didn't find a way of relocating CHAP after compilation, I added a basic one that may prove useful for other people. It enables a user to compile CHAP and install it wherever he wants (that's he normal workflow) and then move the install directory to another place.
--- chap-version_0_9_1/include/config/config.hpp.orig 2018-05-02 13:22:36.000000000 +0200
+++ chap-version_0_9_1/include/config/config.hpp 2019-12-09 12:20:15.276330444 +0100
@@ -25,6 +25,7 @@
#ifndef CONFIG_HPP
#define CONFIG_HPP
+#include <cstdlib>
#include <string>
#include <gromacs/utility/programcontext.h>
@@ -38,7 +39,12 @@
extern "C" inline std::string
chapInstallBase()
{
- return std::string(g_CHAP_INSTALL_BASE);
+ const char* e_CHAP_INSTALL_BASE = std::getenv("CHAP_INSTALL_BASE");
+ if ( e_CHAP_INSTALL_BASE != NULL) {
+ return std::string(e_CHAP_INSTALL_BASE);
+ } else {
+ return std::string(g_CHAP_INSTALL_BASE);
+ }
}
--- chap-version_0_9_1/src/main.cpp.orig 2018-05-02 13:22:36.000000000 +0200
+++ chap-version_0_9_1/src/main.cpp 2019-12-11 20:41:44.217021435 +0100
@@ -21,6 +21,7 @@
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
+#include <limits.h>
#include <vector>
@@ -33,6 +34,20 @@
int main(int argc, char **argv)
{
+ char buf[PATH_MAX];
+ readlink("/proc/self/exe", buf, PATH_MAX - 1);
+
+ // CHAP full binary path
+ std::string fbp(buf);
+ // CHAP install base path
+ std::string ibp = fbp.substr(0, fbp.rfind("/bin/"));
+ // GROMACS GMXLIB path
+ std::string ggp = ibp + "/share/gromacs/top";
+
+ // set environement variables
+ setenv("CHAP_INSTALL_BASE", ibp.c_str(), 0);
+ setenv("GMXLIB", ggp.c_str(), 0);
+
// print front matter:
FrontMatter::print();
Incidentally, I also removed the hardcoded '/chap/' sub-directory because it is more usefull to install a program directly in the prefix provided by the user instead of adding a sub-directory inside that prefix.
--- chap-version_0_9_1/CMakeLists.txt.orig 2018-05-02 13:22:36.000000000 +0200
+++ chap-version_0_9_1/CMakeLists.txt 2019-12-06 21:41:00.975176714 +0100
@@ -175,9 +175,9 @@
#------------------------------------------------------------------------------
# where to install executable on the system:
-install(TARGETS chap DESTINATION ${CMAKE_INSTALL_PREFIX}/chap/bin)
+install(TARGETS chap DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
# also install data and scripts:
-install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/share DESTINATION ${CMAKE_INSTALL_PREFIX}/chap)
-install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/scripts DESTINATION ${CMAKE_INSTALL_PREFIX}/chap USE_SOURCE_PERMISSIONS)
+install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/share DESTINATION ${CMAKE_INSTALL_PREFIX})
+install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/scripts DESTINATION ${CMAKE_INSTALL_PREFIX} USE_SOURCE_PERMISSIONS)
--- chap-version_0_9_1/src/trajectory-analysis/chap_trajectory_analysis.cpp.orig 2018-05-02 13:22:36.000000000 +0200
+++ chap-version_0_9_1/src/trajectory-analysis/chap_trajectory_analysis.cpp 2019-12-09 13:52:36.745685228 +0100
@@ -708,7 +708,7 @@
// base path to location of van-der-Waals radius databases:
std::string radiusFilePath = chapInstallBase() +
- std::string("/chap/share/data/vdwradii/");
+ std::string("/share/data/vdwradii/");
// select appropriate database file:
if( pfVdwRadiusDatabase_ == eVdwRadiusDatabaseHoleAmberuni )
@@ -779,7 +779,7 @@
// base path to location of hydrophobicity databases:
std::string hydrophobicityFilePath = chapInstallBase() +
- std::string("/chap/share/data/hydrophobicity/");
+ std::string("/share/data/hydrophobicity/");
// select appropriate database file:
if( hydrophobicityDatabase_ == eHydrophobicityDatabaseHessa2005 )
@@ -1921,7 +1921,7 @@
// load colour palettes from JSON file:
std::string paletteFilePath = chapInstallBase() +
- std::string("/chap/share/data/palettes/");
+ std::string("/share/data/palettes/");
std::string paletteFileName = paletteFilePath + "default.json";
auto palettes = ColourPaletteProvider::fromJsonFile(paletteFileName);
I hope that will prove usefull,
Cheers.
PS: Patch file with all the previous code :
version_0_9_1_relocation.patch.txt
The PyMol script for loading OBJ files is currently not compatible with the Python3 standard. This might cause errors such as this:
PyMOL>run visualise_pathway.py,main
Traceback (most recent call last):
File "/home/jeffxd/Program/pymol-2.3.2_79/lib/python3.7/site-packages/pymol/parsing.py", line 487, in run
run_(path, ns_main, ns_main)
File "/home/jeffxd/Program/pymol-2.3.2_79/lib/python3.7/site-packages/pymol/parsing.py", line 532, in run_file
execfile(file,global_ns,local_ns)
File "/home/jeffxd/Program/pymol-2.3.2_79/lib/python3.7/site-packages/pymol/parsing.py", line 527, in execfile
exec(co, global_ns, local_ns)
File "visualise_pathway.py", line 89, in <module>
obj = wobj.import_wobj(args.surface)
File "/home/jeffxd/Program/chap-version_0_9_1/examples/example-01/test/wobj.py", line 396, in import_wobj
return obj_importer.read(filename)
File "/home/jeffxd/Program/chap-version_0_9_1/examples/example-01/test/wobj.py", line 182, in read
cgo[key] = self.__create_cgo_object(key)
File "/home/jeffxd/Program/chap-version_0_9_1/examples/example-01/test/wobj.py", line 348, in __create_cgo_object
vertex_a = self.__vertices[face["vert_idx"][0] - 1]
TypeError: 'map' object is not subscriptable
A fix has already been suggested in issue #11.
I'm trying to visualize the tunnel by using the visualise_pathway.py
script that comes with chap. However, I encounter the following error message:
(work) zruan@zruan:~/software/chap/chap/examples/example-03$ pymol
PyMOL(TM) 2.3.4 - Incentive Product
Copyright (C) Schrodinger, LLC
This Executable Build integrates and extends Open-Source PyMOL.
Detected OpenGL version 4.6. Shaders available.
Detected GLSL version 4.60.
OpenGL graphics engine:
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: NVIDIA GeForce GTX 1660 Ti/PCIe/SSE2
GL_VERSION: 4.6.0 NVIDIA 510.73.05
License Expiry date: 19-jul-2023
Detected 24 CPU cores. Enabled multithreaded rendering.
parser: no matching files.
PyMOL>run visualise_pathway.py
Traceback (most recent call last):
File "/home/zruan/software/pymol/lib/python3.7/site-packages/pymol/parsing.py", line 483, in run
run_(path, ns_pymol, ns_pymol)
File "/home/zruan/software/pymol/lib/python3.7/site-packages/pymol/parsing.py", line 532, in run_file
execfile(file,global_ns,local_ns)
File "/home/zruan/software/pymol/lib/python3.7/site-packages/pymol/parsing.py", line 527, in execfile
exec(co, global_ns, local_ns)
File "visualise_pathway.py", line 89, in <module>
obj = wobj.import_wobj(args.surface)
File "/home/zruan/software/chap/chap/examples/example-03/wobj.py", line 396, in import_wobj
return obj_importer.read(filename)
File "/home/zruan/software/chap/chap/examples/example-03/wobj.py", line 182, in read
cgo[key] = self.__create_cgo_object(key)
File "/home/zruan/software/chap/chap/examples/example-03/wobj.py", line 348, in __create_cgo_object
vertex_a = self.__vertices[face["vert_idx"][0] - 1]
TypeError: 'map' object is not subscriptable
Hi sir,
I am trying to install chap 0.9.1 on my workstation which is the Ubuntu 18.04.5 LTS and the gromacs version is 2020.5.
Following the installation guide, I first touch the same issue here, then follow the command below by changing the "set(CMAKE_CXX_STANDARD 11)" to "set(CMAKE_CXX_STANDARD 14)", I can successfully get rid of this error message.
However, when typing the "make" command again, it shows another error below:
[ 6%] Built target googletest
[ 6%] Building CXX object CMakeFiles/chap.dir/src/analysis-setup/residue_information_provider.cpp.o
In file included from /home/joe/Downloads/chap-version_0_9_1/src/analysis-setup/residue_information_provider.cpp:25:0:
/home/joe/Downloads/chap-version_0_9_1/include/analysis-setup/residue_information_provider.hpp:32:10: fatal error: gromacs/topology/atoms.h: No such file or directory
#include <gromacs/topology/atoms.h>
^~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
CMakeFiles/chap.dir/build.make:158: recipe for target 'CMakeFiles/chap.dir/src/analysis-setup/residue_information_provider.cpp.o' failed
make[2]: *** [CMakeFiles/chap.dir/src/analysis-setup/residue_information_provider.cpp.o] Error 1
CMakeFiles/Makefile2:355: recipe for target 'CMakeFiles/chap.dir/all' failed
make[1]: *** [CMakeFiles/chap.dir/all] Error 2
Makefile:140: recipe for target 'all' failed
make: *** [all] Error 2
I am curious if that means my gromacs program just lost the file "atoms.h"? And I should reinstall the gromacs?
Or anything else I should do to fix this error.
Sorry for the interruption, and looking forward to any idea/solution.
Hi,
I am trying to run chap on a 50000 frames trajectory. However the job dies after about 1000 frames, I believe because it feels up all the RAM available on my computer: I can see all the amount of memory used increases until it uses everything.
I have to run it with -dt 100
to have the calculation end successfully. Which means that I loose a significant portion of my MD.
Is this due to a memory leak or other bug? Or does the program needs to keep everything in memory?
Is there a work around this problem? for example is it possible to force writing to disk instead of keeping in memory?
Many thanks in advance.
make
Scanning dependencies of target googletest
[ 0%] Creating directories for 'googletest'
[ 1%] Performing download step (download, verify and extract) for 'googletest'
-- Downloading...
dst='/home/bd422/chap-version_0_9_1/build/googletest-prefix/src/release-1.7.0.zip'
timeout='none'
-- Using src='https://github.com/google/googletest/archive/release-1.7.0.zip'
-- Retrying...
-- Using src='https://github.com/google/googletest/archive/release-1.7.0.zip'
-- Retry after 5 seconds (attempt #2) ...
-- Using src='https://github.com/google/googletest/archive/release-1.7.0.zip'
-- Retry after 5 seconds (attempt #3) ...
-- Using src='https://github.com/google/googletest/archive/release-1.7.0.zip'
-- Retry after 15 seconds (attempt #4) ...
-- Using src='https://github.com/google/googletest/archive/release-1.7.0.zip'
-- Retry after 60 seconds (attempt #5) ...
-- Using src='https://github.com/google/googletest/archive/release-1.7.0.zip'
CMake Error at googletest-stamp/download-googletest.cmake:159 (message):
Each download failed!
error: downloading 'https://github.com/google/googletest/archive/release-1.7.0.zip' failed
status_code: 1
status_string: "Unsupported protocol"
log:
--- LOG BEGIN ---
Protocol "https" not supported or disabled in libcurl
Closing connection -1
--- LOG END ---
error: downloading 'https://github.com/google/googletest/archive/release-1.7.0.zip' failed
status_code: 1
status_string: "Unsupported protocol"
log:
--- LOG BEGIN ---
Protocol "https" not supported or disabled in libcurl
Closing connection -1
--- LOG END ---
error: downloading 'https://github.com/google/googletest/archive/release-1.7.0.zip' failed
status_code: 1
status_string: "Unsupported protocol"
log:
--- LOG BEGIN ---
Protocol "https" not supported or disabled in libcurl
Closing connection -1
--- LOG END ---
error: downloading 'https://github.com/google/googletest/archive/release-1.7.0.zip' failed
status_code: 1
status_string: "Unsupported protocol"
log:
--- LOG BEGIN ---
Protocol "https" not supported or disabled in libcurl
Closing connection -1
--- LOG END ---
error: downloading 'https://github.com/google/googletest/archive/release-1.7.0.zip' failed
status_code: 1
status_string: "Unsupported protocol"
log:
--- LOG BEGIN ---
Protocol "https" not supported or disabled in libcurl
Closing connection -1
--- LOG END ---
error: downloading 'https://github.com/google/googletest/archive/release-1.7.0.zip' failed
status_code: 1
status_string: "Unsupported protocol"
log:
--- LOG BEGIN ---
Protocol "https" not supported or disabled in libcurl
Closing connection -1
--- LOG END ---
CMakeFiles/googletest.dir/build.make:90: recipe for target 'googletest-prefix/src/googletest-stamp/googletest-download' failed
make[2]: *** [googletest-prefix/src/googletest-stamp/googletest-download] Error 1
CMakeFiles/Makefile2:404: recipe for target 'CMakeFiles/googletest.dir/all' failed
make[1]: *** [CMakeFiles/googletest.dir/all] Error 2
Makefile:140: recipe for target 'all' failed
make: *** [all] Error 2
I'm trying to install CHAP version_0_9_1 and during the make command, I get this error:
(python3.11) bburendei@solaire:~/apps/CHAP/chap-version_0_9_1/build$ make
[ 6%] Built target googletest
Consolidate compiler generated dependencies of target chap
[ 7%] Building CXX object CMakeFiles/chap.dir/src/aggregation/multiscalar_time_series.cpp.o
/home/bburendei/apps/CHAP/chap-version_0_9_1/src/aggregation/multiscalar_time_series.cpp: In member function ‘void MultiscalarTimeSeries::addScalarTimeSeries(const ScalarTimeSeries&)’:
/home/bburendei/apps/CHAP/chap-version_0_9_1/src/aggregation/multiscalar_time_series.cpp:56:28: error: ‘logic_error’ is not a member of ‘std’
56 | throw std::logic_error("Time stamps of new time series do "
| ^~~~~~~~~~~
/home/bburendei/apps/CHAP/chap-version_0_9_1/src/aggregation/multiscalar_time_series.cpp:72:24: error: ‘logic_error’ is not a member of ‘std’
72 | throw std::logic_error("Multiscalar time series can not accept "
| ^~~~~~~~~~~
make[2]: *** [CMakeFiles/chap.dir/build.make:90: CMakeFiles/chap.dir/src/aggregation/multiscalar_time_series.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:391: CMakeFiles/chap.dir/all] Error 2
make: *** [Makefile:146: all] Error 2
I managed to install GROMACS 2018 with the FFTPACK library
I can't find previous issues detailing this, so I'm a bit lost as to what I should do to fix this.
Thanks in advance.
Batuujin
When building 0.9.1 with LAPACK installed in a non-standard location, the link flags for LAPACKE_LIBRARIES don't get correctly propagated to linking the chap
binary, resulting in link errors.
Patching this results in additional link errors for libgfortran
(at least with gcc 4.9.3 on CentOS 6), suggesting that there may be glitches in the FORTRANSUPPORTLIB
section of cmake/Modules/FindLAPACKE/FindLAPACKE.cmake
Hello,
I have been recently calculating the pore profile of a membrane protein, and I encountered an error:
chap -f closed.pdb -s closed.pdb -hydrophob-database user -hydrophob-json colour_scal.json
Standard library runtime error (possible bug):
(exception type: St13runtime_error)
Pore radius at initial probe position is infinite. Consider increasing the
maximum pore radius with -pf-max-free-dist or set an appropriate cutoff for
neighbourhood searches explicitly with -pf-cutoff.
While adjusting the cutoff distance, I noticed that it doesn't generate the appropriate radius. To verify this, I tried HOLE, and it does generate the radii. If I choose the selection(chap) of alpha carbon or side chain, it gives me truncated and large radii, approximately 20 Å. I am using the following command:
chap -f closed.pdb -s closed.pdb -hydrophob-database user -hydrophob-json colour_scal.json -pf-max-free-dist 2 # 2-100
Could you please help me identify if I am missing any steps?
Regards,
Aashish
CMakeFiles/googletest.dir/build.make:90: recipe for target 'googletest-prefix/src/googletest-stamp/googletest-download' failed
make[2]: *** [googletest-prefix/src/googletest-stamp/googletest-download] Error 1
CMakeFiles/Makefile2:429: recipe for target 'CMakeFiles/googletest.dir/all' failed
make[1]: *** [CMakeFiles/googletest.dir/all] Error 2
Makefile:140: recipe for target 'all' failed
make: *** [all] Error 2
Hello,
Great tool you have built, thank you very much.
I have compiled in a VM, and had it working on some small scale data, but have recently been getting this error;
"Program: chap, version 2018
Standard library runtime error (possible bug):
(exception type: St13runtime_error)
Number of frames read does not equal number of frames analyised.
"
Any ideas what this could mean?
Best,
Jonah
Hello,
I have tried running CHAP with this command:
chap -f ../../solvated_pores.trr -s ../../solvated_pores.pdb -sel-pathway 1 -sel-solvent 'Water' -pf-cutoff 0 -pf-init-probe-pos 133 112 70
If I set the initial probe position as I do above, it reads all the frames but does not produce a correct output.
trr version: GMX_trn_file (single precision)
Reading frame 1900 time 190.000
Analyzed 2000 frames, last time 199.900
Forming time averages, 100% completee
-------------------------------------------------------
Program: chap, version 2016.6
Standard library logic error (bug):
(exception type: St12out_of_range)
vector::_M_range_check: __n (which is 2) >= this->size() (which is 2)
By this, I mean that it produces an output.pdb
and output.json
but not output.obj
or output.mtl
. However, if I run the same command but do not specify the initial probe position, it runs properly. I need some way of annotating different ion channels in my system, which I am currently trying to do by starting the probe in different positions. I cannot find much information online about this error, do you know how to fix it? Thanks!
Best regards,
Christian
It seems that I am facing a problem with the way the pore facing residues are selected by chap.
Basically running the program on my protein returns a zero-array for the list of pore facing residues.
To be able to generate a plot like the "radius_profile.png" example, I need to use the pore lining residues data["residueSummary"]["poreFacing"]
but then I get most of the residues of my protein.
I tried to change the selection string from "name CA" to "name CB" or include more atoms for example but without success.
This is not much of a problem for my current project but I thought it would be worth mentioning that the way the pore facing residues are identified do not always work.
Hello,
I am trying to install chap on an Ubuntu 16.04 computer. I have a fresh build of Gromacs 2018 and installed the dependancies following the instruction provided in the chap documentation, namely: sudo apt-get install libblas-dev liblapacke-dev libatlas-base-dev
Here is the result of cmake
:
-- The CXX compiler identification is GNU 5.4.0
-- The C compiler identification is GNU 5.4.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Boost version: 1.58.0
-- Found LAPACKE: /usr/include
-- Found GROMACS: 2018.7
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
-- Generating done
-- Build files have been written to: /home/el14718/Software/chap-version_0_9_1/build
And here is the error following make
:
[...]
[ 42%] Building CXX object CMakeFiles/chap.dir/src/statistics/weighted_kernel_density_estimator.cpp.o
[ 43%] Building CXX object CMakeFiles/chap.dir/src/statistics/kernel_density_estimator.cpp.o
[ 43%] Building CXX object CMakeFiles/chap.dir/config/version.cpp.o
[ 44%] Building CXX object CMakeFiles/chap.dir/config/config.cpp.o
[ 45%] Linking CXX executable chap
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `sggev3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `sbdsvdx_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `cgesvj_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `dgetrf2_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `dpotrf2_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `sggsvp3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `zgges3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `cgesvdx_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `zggev3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `dgesvdx_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `cggsvp3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `zggsvp3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `sgges3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `sgesvdx_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `zgesvdx_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `dbdsvdx_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `cgghd3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `dggsvp3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `cggev3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `spotrf2_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `sggsvd3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `zpotrf2_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `dgghd3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `sgetrf2_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `zgghd3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `cgejsv_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `dggsvd3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `cpotrf2_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `cggsvd3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `dggev3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `zgejsv_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `sgghd3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `zggsvd3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `cgetrf2_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `cgges3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `zgesvj_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `dgges3_'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib/liblapacke.so: undefined reference to `zgetrf2_'
collect2: error: ld returned 1 exit status
CMakeFiles/chap.dir/build.make:1374: recipe for target 'chap' failed
make[2]: *** [chap] Error 1
CMakeFiles/Makefile2:392: recipe for target 'CMakeFiles/chap.dir/all' failed
make[1]: *** [CMakeFiles/chap.dir/all] Error 2
Makefile:138: recipe for target 'all' failed
make: *** [all] Error 2
Do you have any idea what the problem could be? Do you know how it could be fixed?
Is it a problem relating the the latest version of Lapack?
Many thanks in advance for your help!
Eric
Hello,
I am Aashish, and I am calculating channel pore profiles using Chap. I have installed Chap using Anaconda.
I have successfully generated the pore output files, but when I visualize the pore in VMD using both the tcl script "visualise_pathway.tcl" and "wobj.tcl", the protein pore profile is always in white color, whereas the pore residue is orange and yellow.
Do I miss something?
I am using the following command:
chap -f protein.xtc -s protein.pdb --sel-pathway 1
Regards,
Aashish
The weblink "http://www.channotation.org/" is down.
In file included from /home/vrdl/Downloads/chap-master/src/aggregation/boltzmann_energy_calculator.cpp:25:
/home/vrdl/Downloads/chap-master/include/aggregation/boltzmann_energy_calculator.hpp:30:10: fatal error: gromacs/utility/real.h: No such file or directory
30 | #include "gromacs/utility/real.h"
| ^~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/chap.dir/build.make:63: CMakeFiles/chap.dir/src/aggregation/boltzmann_energy_calculator.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:559: CMakeFiles/chap.dir/all] Error 2
make: *** [Makefile:141: all] Error 2
Hi CHAP team,
I have 2 CHAP profiles for two aligned ion channels.
The channels are different in height and therefore have different centres of mass but their channels are aligned. when I plot their profiles they are not aligned, presumably because of the difference in them COMs.
I typically plot the radius against data["pathwayProfile"]["s"]
. Would it be possible to plot against the z-coordinate? All simulation frames are aligned
Thanks
Hi,
I have been trying to compile CHAP on our local cluster but ran into a number of issues.
First the I encountered the same problem as described in #5
However, the suggested fix didn't work (Adding include_directories(${LAPACKE_INCLUDE_DIRS})
or target_include_directories(chap PUBLIC ${LAPACKE_INCLUDE_DIRS})
to CMakeLists.txt
). Instead I had to add the explicit path to CMakeLists.txt
(I am mainly mentioning it in case others run into the same problem).
I have however further problems during compuilation. With an intel compiler (which was used to compile Gromacs), I get the following error:
[ 42%] Building CXX object CMakeFiles/chap.dir/src/statistics/weighted_kernel_density_estimator.cpp.o
[ 43%] Building CXX object CMakeFiles/chap.dir/src/trajectory-analysis/chap_trajectory_analysis.cpp.o
/mnt/storage/home/el14718/el14718/SOFTWARE/chap-version_0_9_1/src/trajectory-analysis/chap_trajectory_analysis.cpp(87): error #3291: invalid narrowing conversion from "double" to "float"
pfInitProbePos_ = {std::nan(""), std::nan(""), std::nan("")};
^
/mnt/storage/home/el14718/el14718/SOFTWARE/chap-version_0_9_1/src/trajectory-analysis/chap_trajectory_analysis.cpp(87): error #3291: invalid narrowing conversion from "double" to "float"
pfInitProbePos_ = {std::nan(""), std::nan(""), std::nan("")};
^
/mnt/storage/home/el14718/el14718/SOFTWARE/chap-version_0_9_1/src/trajectory-analysis/chap_trajectory_analysis.cpp(87): error #3291: invalid narrowing conversion from "double" to "float"
pfInitProbePos_ = {std::nan(""), std::nan(""), std::nan("")};
^
/mnt/storage/home/el14718/el14718/SOFTWARE/chap-version_0_9_1/src/trajectory-analysis/chap_trajectory_analysis.cpp(1633): warning #192: unrecognized character escape sequence
<<"\% complete"
^
/mnt/storage/home/el14718/el14718/SOFTWARE/chap-version_0_9_1/src/trajectory-analysis/chap_trajectory_analysis.cpp(1775): warning #192: unrecognized character escape sequence
<<"\% complete"
^
compilation aborted for /mnt/storage/home/el14718/el14718/SOFTWARE/chap-version_0_9_1/src/trajectory-analysis/chap_trajectory_analysis.cpp (code 2)
make[2]: *** [CMakeFiles/chap.dir/src/trajectory-analysis/chap_trajectory_analysis.cpp.o] Error 2
make[1]: *** [CMakeFiles/chap.dir/all] Error 2
make: *** [all] Error 2
So I tried to switch to gcc, but then I got this error:
[ 44%] Building CXX object CMakeFiles/chap.dir/config/config.cpp.o
[ 45%] Linking CXX executable chap
c++: error: unrecognized command line option '-qopenmp'; did you mean '-fopenmp'?
make[2]: *** [chap] Error 1
make[1]: *** [CMakeFiles/chap.dir/all] Error 2
make: *** [all] Error 2
I thought it could be a problem of gcc version (I used GCC 7.2.0) so I tried with the same GCC version (5.4.0) as the one used on my desktop for with the installation was a success (Ubuntu desktop with all prerequisite libraries installed with apt-get).
Do you have any ideas on how to fix it?
I am happy to replace -qopenmp
with -fopenmp
but I don't know where to change it.
Many thanks
Hi,
Thanks for making that program available.
I tried to convert the json to csv, but it looks like the "/chap_json2csv.py " mentioned in the documentation is not part of the latest version. Is it possible to receive it in some way?
Thanks,
Best,
Nicolas
Will it be possible to have conda package so it is easier to install all dependencies?
I am having this error:
Unable to find the Boost header files. Please set BOOST_ROOT to the root
directory containing Boost or BOOST_INCLUDEDIR to the directory containing
Boost's headers.
Call Stack (most recent call first):
CMakeLists.txt:60 (find_package)
Could NOT find LAPACKE (missing: LAPACKE_CBLAS_INCLUDE_DIR
LAPACKE_LAPACKE_INCLUDE_DIR)
Hi,
I am trying to compile CHAP but keep running into one issue after another.
this is the one I am getting with gcc 6.3 and gmx 2019.3
chap/src/analysis-setup/residue_information_provider.cpp:25:0:
chap/include/analysis-setup/residue_information_provider.hpp:67:42: error: ‘TopologyInformation’ in namespace ‘gmx’ does not name a type
void nameFromTopology(const gmx::TopologyInformation &top);
I checked gromacs source there is a TopologyIformation class in there, I am assuming the version change should have changed something here.
compile well with gromacs 2018.6. So that is a version change issue for sure.
Hi,
After a lengthy compilation process, I was able to finish compilation and I tested the program with the given example.
It was giving me the error in the topic with the standard command but when I added "-out-num-points 1000", it worked. Here is the command I issued to run it:
chap -f 4pirtm.xtc -s 4pirtm.tpr -out-filename test -out-num-points 1000
I did the same with my own protein but it gave exactly the same error.
Any suggestion about the possible reason?
Hi Inniag,
When trying to install CHAP on CentOS 7 linux (with GROMACS 2018.8, Intel Compilers 2018.3 and Intel MKL 2018.3) I had to fix a few issues and bugs for making it work correctly.
--- chap-version_0_9_1/src/trajectory-analysis/chap_trajectory_analysis.cpp.orig 2018-05-02 13:22:36.000000000 +0200
+++ chap-version_0_9_1/src/trajectory-analysis/chap_trajectory_analysis.cpp 2019-12-09 13:52:36.745685228 +0100
@@ -84,7 +84,7 @@
frameStreamData_.setMultipoint(true);
// default initial probe position and chanell direction:
- pfInitProbePos_ = {std::nan(""), std::nan(""), std::nan("")};
+ pfInitProbePos_ = {(real)std::nan(""), (real)std::nan(""), (real)std::nan("")};
pfChanDirVec_ = {0.0, 0.0, 1.0};
}
--- chap-version_0_9_1/test/geometry/ut_bspline_basis_set.cpp.orig 2018-05-02 13:22:36.000000000 +0200
+++ chap-version_0_9_1/test/geometry/ut_bspline_basis_set.cpp 2019-12-06 16:57:13.304949817 +0100
@@ -41,7 +41,7 @@
std::vector<real> uniqueKnots_ = {-4, -0.5, 0.0, 0.5, 4};
// evaluation points:
- std::vector<real> evalPoints_ = {-4.0, -2.5, 0.0, 0.5, -1.0, std::sqrt(2.0), 4.0};
+ std::vector<real> evalPoints_ = {-4.0, -2.5, 0.0, 0.5, -1.0, (real)std::sqrt(2.0), 4.0};
// true knot span index:
std::vector<size_t> knotSpanIdx_ = {0, 0, 2, 3, 0, 3, 3};
--- chap-version_0_9_1/test/statistics/ut_amise_optimal_bandwidth_estimator.cpp.orig 2018-05-02 13:22:36.000000000 +0200
+++ chap-version_0_9_1/test/statistics/ut_amise_optimal_bandwidth_estimator.cpp 2019-12-06 16:59:40.880202641 +0100
@@ -62,7 +62,7 @@
// parameters:
int numReps = 2;
- std::vector<real> mean = {-10, 0.0, std::sqrt(2.0)};
+ std::vector<real> mean = {-10, 0.0, (real)std::sqrt(2.0)};
std::vector<real> numSamples = {250, 500, 750};
std::vector<real> standardDeviation = {100.0, 1.0, 0.01};
--- chap-version_0_9_1/test/statistics/ut_histogram_density_estimator.cpp.orig 2018-05-02 13:22:36.000000000 +0200
+++ chap-version_0_9_1/test/statistics/ut_histogram_density_estimator.cpp 2019-12-06 17:07:42.104516814 +0100
@@ -82,7 +82,7 @@
HistogramDensityEstimator hde;
// some bin widths to try:
- std::vector<real> binWidth = {1.0, 0.1, 1e-5, std::sqrt(2.0)};
+ std::vector<real> binWidth = {1.0, 0.1, 1e-5, (real)std::sqrt(2.0)};
// loop over bin widths and check that breaks are correct:
for(auto it = binWidth.begin(); it != binWidth.end(); it++)
@@ -138,7 +138,7 @@
// some bin widths to try:
// NOTE: if bin width too small, spline interpolation will fail!
- std::vector<real> binWidth = {1.0, 0.1, 1e-2, 0.1*std::sqrt(2.0)};
+ std::vector<real> binWidth = {1.0, 0.1, 1e-2, (real)(0.1*std::sqrt(2.0))};
// perform tests for each bin width value:
for(auto bw : binWidth)
@@ -187,7 +187,7 @@
// some bin widths to try:
// NOTE: if bin width too small, spline interpolation will fail!
- std::vector<real> binWidth = {1.0, 0.1, 1e-2, 0.1*std::sqrt(2.0)};
+ std::vector<real> binWidth = {1.0, 0.1, 1e-2, (real)(0.1*std::sqrt(2.0))};
// perform tests for each binwidth value:
for(auto bw : binWidth)
@@ -238,8 +238,8 @@
// some bin widths to try:
// NOTE: if bin width too small, spline interpolation will fail!
- std::vector<real> binWidth = {1.0, 0.1, 1e-2, 0.1*std::sqrt(2.0)};
- binWidth = {1.0, 0.1, 0.01, 0.1*std::sqrt(2.0)};
+ std::vector<real> binWidth = {1.0, 0.1, 1e-2, (real)(0.1*std::sqrt(2.0))};
+ binWidth = {1.0, 0.1, 0.01, (real)(0.1*std::sqrt(2.0))};
// get data range:
real dataMin = *std::min_element(testData_.begin(), testData_.end());
@@ -268,7 +268,7 @@
0);
// this should always be zero:
- ASSERT_NEAR(0.0, density, std::sqrt(eps));
+ ASSERT_NEAR(0.0, density, (real)std::sqrt(eps));
}
// evaluate density below data range:
@@ -283,7 +283,7 @@
0);
// this should always be zero:
- ASSERT_NEAR(0.0, density, std::sqrt(eps));
+ ASSERT_NEAR(0.0, density, (real)std::sqrt(eps));
}
// evaluate spline within data range:
@@ -317,7 +317,7 @@
integral += d;
}
integral *= evalStep;
- ASSERT_NEAR(1.0, integral, std::sqrt(eps));
+ ASSERT_NEAR(1.0, integral, (real)std::sqrt(eps));
}
}
--- chap-version_0_9_1/test/statistics/ut_summary_statistics.cpp.orig 2018-05-02 13:22:36.000000000 +0200
+++ chap-version_0_9_1/test/statistics/ut_summary_statistics.cpp 2019-12-06 17:16:08.457527879 +0100
@@ -44,7 +44,7 @@
// constructor for creating test data:
SummaryStatisticsTest()
{
- testData_ = {0.3, 1.5, -0.9, std::sqrt(2.0), -5.1};
+ testData_ = {0.3, 1.5, -0.9, (real)std::sqrt(2.0), -5.1};
}
--- chap-version_0_9_1/test/statistics/ut_gaussian_density_derivative.cpp.orig 2018-05-02 13:22:36.000000000 +0200
+++ chap-version_0_9_1/test/statistics/ut_gaussian_density_derivative.cpp 2019-12-06 17:24:42.659436050 +0100
@@ -263,9 +263,9 @@
// check that truncation criterion is met:
real b = std::min<real>(gdd.rc_,
- 0.5*(gdd.ri_ + std::sqrt(gdd.ri_*gdd.ri_ +
+ 0.5*(gdd.ri_ + (real)std::sqrt(gdd.ri_*gdd.ri_ +
8.0*trunc*gdd.bw_*gdd.bw_)));
- real error = std::sqrt(gdd.factorial(gdd.r_))
+ real error = (real)std::sqrt(gdd.factorial(gdd.r_))
/ gdd.factorial(trunc)
* std::pow((gdd.ri_ * b / (gdd.bw_*gdd.bw_)), trunc)
* std::exp(-(std::pow(gdd.ri_ - b, 2))
--- chap-version_0_9_1/test/geometry/ut_basis_spline.cpp.orig 2018-05-02 13:22:36.000000000 +0200
+++ chap-version_0_9_1/test/geometry/ut_basis_spline.cpp 2019-12-10 18:55:53.114400365 +0100
@@ -49,7 +49,7 @@
std::vector<real> knotVector_ = {-4, -0.5, 0.0, 0.5, 4};
// evaluation points:
- std::vector<real> evalPoints_ = {-4.0, -2.5, 0.0, 0.5, -1.0, std::sqrt(2.0), 4.0};
+ std::vector<real> evalPoints_ = {-4.0, -2.5, 0.0, 0.5, -1.0, (real)std::sqrt(2.0), 4.0};
};
--- chap-version_0_9_1/src/io/analysis_data_json_frame_exporter.cpp.orig 2018-05-02 13:22:36.000000000 +0200
+++ chap-version_0_9_1/src/io/analysis_data_json_frame_exporter.cpp 2019-12-10 18:45:48.496459218 +0100
@@ -169,7 +169,7 @@
const gmx::AnalysisDataFrameHeader& /*frame*/)
{
// open output file separately for each frame:
- file_.open(fileName_.c_str(), std::fstream::app);
+ file_.open(fileName_.c_str(), std::fstream::out | std::fstream::app);
// create buffer writer string writer:
rapidjson::StringBuffer buffer;
--- chap-version_0_9_1/src/io/molecular_path_obj_exporter.cpp.orig 2018-05-02 13:22:36.000000000 +0200
+++ chap-version_0_9_1/src/io/molecular_path_obj_exporter.cpp 2019-12-10 21:33:58.590351428 +0100
@@ -1064,7 +1064,7 @@
// for sequential colour scale, shift data to positive real range and
// scale by length of data interval:
real shift = -minProp;
- real scale = 1.0/(maxProp - minProp);
+ double scale = 1.0/(maxProp - minProp);
// shift and scale the property array:
std::for_each(prop.begin(), prop.end(), [shift](real &p){p += shift;});
@@ -1075,7 +1075,7 @@
// for divergent colour scale, scale both positive and negative values
// such that data lies in [-0.5, 0.5], then shift by 0.5:
real shift = 0.5;
- real scale = 1.0/std::max(std::fabs(minProp), std::fabs(maxProp))/2.0;
+ double scale = 1.0/std::max(std::fabs(minProp), std::fabs(maxProp))/2.0;
// scale and shift:
std::for_each(prop.begin(), prop.end(), [scale](real &p){p *= scale;});
That is all for the bug fixes,
Cheers.
PS: patch file with all the previous fixes inside :
version_0_9_1_fixes.patch.txt
Hi everyone,
I am trying to install Chap (Version 0.9.1) on my Computer (Ubuntu 20.04.2 LTS). When I run make, I get the following error:
####################################################################################################
[ 8%] Building CXX object CMakeFiles/chap.dir/src/aggregation/number_density_calculator.cpp.o
In file included from /usr/local/gromacs/include/gromacs/math/vec.h:111,
from /home/theres/THERES_projects/tools/chap-version_0_9_1/include/geometry/spline_curve_1D.hpp:33,
from /home/theres/THERES_projects/tools/chap-version_0_9_1/include/aggregation/number_density_calculator.hpp:32,
from /home/theres/THERES_projects/tools/chap-version_0_9_1/src/aggregation/number_density_calculator.cpp:29:
/usr/local/gromacs/include/gromacs/math/vectypes.h:96:41: error: ‘remove_cv_t’ is not a member of ‘std’
static_assert(!std::is_pointer<std::remove_cv_t>::value,
^~~~~~~~~~~
/usr/local/gromacs/include/gromacs/math/vectypes.h:96:41: note: suggested alternative: ‘remove_cv’
static_assert(!std::is_pointer<std::remove_cv_t>::value,
^~~~~~~~~~~
remove_cv
/usr/local/gromacs/include/gromacs/math/vectypes.h:96:41: error: ‘remove_cv_t’ is not a member of ‘std’
/usr/local/gromacs/include/gromacs/math/vectypes.h:96:41: note: suggested alternative: ‘remove_cv’
static_assert(!std::is_pointer<std::remove_cv_t>::value,
^~~~~~~~~~~
remove_cv
/usr/local/gromacs/include/gromacs/math/vectypes.h:96:53: error: template argument 1 is invalid
static_assert(!std::is_pointer<std::remove_cv_t>::value,
^~~~~~~~~
/usr/local/gromacs/include/gromacs/math/vectypes.h:96:66: error: ‘::value’ has not been declared
static_assert(!std::is_pointer<std::remove_cv_t>::value,
^~~~~
/usr/local/gromacs/include/gromacs/math/vectypes.h:96:66: note: suggested alternative: ‘valloc’
static_assert(!std::is_pointer<std::remove_cv_t>::value,
^~~~~
valloc
In file included from /home/theres/THERES_projects/tools/chap-version_0_9_1/include/geometry/spline_curve_1D.hpp:33,
from /home/theres/THERES_projects/tools/chap-version_0_9_1/include/aggregation/number_density_calculator.hpp:32,
from /home/theres/THERES_projects/tools/chap-version_0_9_1/src/aggregation/number_density_calculator.cpp:29:
/usr/local/gromacs/include/gromacs/math/vec.h:630:6: error: ‘remove_const_t’ in namespace ‘std’ does not name a template type
std::remove_const_t norm(T* v)
^~~~~~~~~~~~~~
/usr/local/gromacs/include/gromacs/math/vec.h:630:1: note: suggested alternative: ‘remove_const’
std::remove_const_t norm(T* v)
^~~
remove_const
/usr/local/gromacs/include/gromacs/math/vec.h:635:6: error: ‘remove_const_t’ in namespace ‘std’ does not name a template type
std::remove_const_t norm2(T* v)
^~~~~~~~~~~~~~
/usr/local/gromacs/include/gromacs/math/vec.h:635:1: note: suggested alternative: ‘remove_const’
std::remove_const_t norm2(T* v)
^~~
remove_const
make[2]: *** [CMakeFiles/chap.dir/build.make:104: CMakeFiles/chap.dir/src/aggregation/number_density_calculator.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:547: CMakeFiles/chap.dir/all] Error 2
make: *** [Makefile:146: all] Error 2
######################################################################################################
######################################################################################################
I have installed GROMACS 2020.6 with an external fftw library.
In case you need the cmake command I ran for GMX installation:
sudo cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-11.2/ -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Debug -DCMAKE_C_COMPILER=/usr/bin/gcc-8 -DBUILD_SHARED_LIBS=OFF
Other information you might need:
######################################################################################################
I am not sure what I am doing wrong and I would be very grateful for any tips or tricks how to deal with this this error. Thank you very much in advance!
I have some trajectories produced using NAMD. I have tried to convert these to a form that will work in CHAP and failed. Is there a way to convert these trajectories to a format that is readable by CHAP?
Thank you in advance.
Vern Winston
Gianni,
I had the idea to include charge as a function of the pore profile averaged over the trajectory. This will actually be a feature useful for pores with a charge filters. All it would entitle is keeping track of the sum of partial charges in each bin, which is already part of the topology.
Let me know what you think, I would be happy to make these additions.
Best
Jerome
I noticed an issue when building with a BOOST library that is installed in a non-standard location. I can get cmake to pick it up by setting -DBOOST_ROOT=/path/to/boost
, but when I execute make
it fails at some point because the compiler doesn't find the header files:
$ cmake .. -DBOOST_ROOT=$BOOST_HOME
-- The CXX compiler identification is GNU 7.3.0
-- The C compiler identification is GNU 7.3.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Boost version: 1.68.0
-- Found LAPACKE: /usr/include/x86_64-linux-gnu
-- Found GROMACS: 2018.4
CMake Warning at /opt/tcbsys/gromacs/2018.4/AVX2_256/share/cmake/gromacs/gromacs-config.cmake:132 (message):
You are compiling with a different C++ compiler from the one that was used
to compile GROMACS. This may lead to linking or runtime problems. GROMACS
was compiled with GNU 5.4.0 (/usr/bin/g++-5).
Call Stack (most recent call first):
CMakeLists.txt:87 (gromacs_check_compiler)
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/src/chap-version_0_9_1/build
$ make
Scanning dependencies of target googletest
[ 0%] Creating directories for 'googletest'
[ 1%] Performing download step (download, verify and extract) for 'googletest'
-- Downloading...
dst='/tmp/src/chap-version_0_9_1/build/googletest-prefix/src/release-1.7.0.zip'
timeout='none'
-- Using src='https://github.com/google/googletest/archive/release-1.7.0.zip'
-- [download 0% complete]
[...]
-- [download 100% complete]
-- Downloading... done
-- extracting...
src='/tmp/src/chap-version_0_9_1/build/googletest-prefix/src/release-1.7.0.zip'
dst='/tmp/src/chap-version_0_9_1/build/googletest-prefix/src/googletest'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 2%] No patch step for 'googletest'
[ 3%] No update step for 'googletest'
[ 3%] Performing configure step for 'googletest'
-- The CXX compiler identification is GNU 7.3.0
-- The C compiler identification is GNU 7.3.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Found PythonInterp: /usr/bin/python (found version "2.7.15")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/src/chap-version_0_9_1/build/googletest-prefix/src/googletest-build
[ 4%] Performing build step for 'googletest'
Scanning dependencies of target gtest
[ 25%] Building CXX object CMakeFiles/gtest.dir/src/gtest-all.cc.o
[ 50%] Linking CXX static library libgtest.a
[ 50%] Built target gtest
Scanning dependencies of target gtest_main
[ 75%] Building CXX object CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
[100%] Linking CXX static library libgtest_main.a
[100%] Built target gtest_main
[ 5%] No install step for 'googletest'
[ 6%] Completed 'googletest'
[ 6%] Built target googletest
Scanning dependencies of target chap
[ 6%] Building CXX object CMakeFiles/chap.dir/src/aggregation/boltzmann_energy_calculator.cpp.o
[ 7%] Building CXX object CMakeFiles/chap.dir/src/aggregation/multiscalar_time_series.cpp.o
[ 8%] Building CXX object CMakeFiles/chap.dir/src/aggregation/number_density_calculator.cpp.o
[ 9%] Building CXX object CMakeFiles/chap.dir/src/aggregation/scalar_time_series.cpp.o
[ 9%] Building CXX object CMakeFiles/chap.dir/src/analysis-setup/residue_information_provider.cpp.o
[ 10%] Building CXX object CMakeFiles/chap.dir/src/config/back_matter.cpp.o
[ 11%] Building CXX object CMakeFiles/chap.dir/src/config/front_matter.cpp.o
[ 12%] Building CXX object CMakeFiles/chap.dir/src/geometry/abstract_cubic_spline_interp.cpp.o
[ 12%] Building CXX object CMakeFiles/chap.dir/src/geometry/abstract_spline_curve.cpp.o
[ 13%] Building CXX object CMakeFiles/chap.dir/src/geometry/basis_spline.cpp.o
[ 14%] Building CXX object CMakeFiles/chap.dir/src/geometry/bspline_basis_set.cpp.o
[ 15%] Building CXX object CMakeFiles/chap.dir/src/geometry/cubic_spline_interp_1D.cpp.o
[ 16%] Building CXX object CMakeFiles/chap.dir/src/geometry/cubic_spline_interp_3D.cpp.o
[ 16%] Building CXX object CMakeFiles/chap.dir/src/geometry/linear_spline_interp_1D.cpp.o
[ 17%] Building CXX object CMakeFiles/chap.dir/src/geometry/spline_curve_1D.cpp.o
/tmp/src/chap-version_0_9_1/src/geometry/spline_curve_1D.cpp:28:10: fatal error: boost/math/tools/minima.hpp: No such file or directory
#include <boost/math/tools/minima.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
CMakeFiles/chap.dir/build.make:398: recipe for target 'CMakeFiles/chap.dir/src/geometry/spline_curve_1D.cpp.o' failed
make[2]: *** [CMakeFiles/chap.dir/src/geometry/spline_curve_1D.cpp.o] Error 1
CMakeFiles/Makefile2:355: recipe for target 'CMakeFiles/chap.dir/all' failed
make[1]: *** [CMakeFiles/chap.dir/all] Error 2
Makefile:140: recipe for target 'all' failed
make: *** [all] Error 2
Running make in verbose mode shows that the compiler command line is missing the flag -I/path/to/boost/include
:
$ make VERBOSE=1
/usr/bin/cmake -H/tmp/src/chap-version_0_9_1 -B/tmp/src/chap-version_0_9_1/build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /tmp/src/chap-version_0_9_1/build/CMakeFiles /tmp/src/chap-version_0_9_1/build/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/tmp/src/chap-version_0_9_1/build'
make -f CMakeFiles/googletest.dir/build.make CMakeFiles/googletest.dir/depend
make[2]: Entering directory '/tmp/src/chap-version_0_9_1/build'
cd /tmp/src/chap-version_0_9_1/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/src/chap-version_0_9_1 /tmp/src/chap-version_0_9_1 /tmp/src/chap-version_0_9_1/build /tmp/src/chap-version_0_9_1/build /tmp/src/chap-version_0_9_1/build/CMakeFiles/googletest.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/tmp/src/chap-version_0_9_1/build'
make -f CMakeFiles/googletest.dir/build.make CMakeFiles/googletest.dir/build
make[2]: Entering directory '/tmp/src/chap-version_0_9_1/build'
make[2]: Nothing to be done for 'CMakeFiles/googletest.dir/build'.
make[2]: Leaving directory '/tmp/src/chap-version_0_9_1/build'
[ 6%] Built target googletest
make -f CMakeFiles/chap.dir/build.make CMakeFiles/chap.dir/depend
make[2]: Entering directory '/tmp/src/chap-version_0_9_1/build'
cd /tmp/src/chap-version_0_9_1/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/src/chap-version_0_9_1 /tmp/src/chap-version_0_9_1 /tmp/src/chap-version_0_9_1/build /tmp/src/chap-version_0_9_1/build /tmp/src/chap-version_0_9_1/build/CMakeFiles/chap.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/tmp/src/chap-version_0_9_1/build'
make -f CMakeFiles/chap.dir/build.make CMakeFiles/chap.dir/build
make[2]: Entering directory '/tmp/src/chap-version_0_9_1/build'
[ 7%] Building CXX object CMakeFiles/chap.dir/src/geometry/spline_curve_1D.cpp.o
/usr/bin/c++ -DGMX_DOUBLE=0 -DRAPIDJSON_HAS_STDSTRING -I/opt/tcbsys/gromacs/2018.4/AVX2_256/include -I/tmp/src/chap-version_0_9_1/build/googletest-prefix/src/googletest/include -I/tmp/src/chap-version_0_9_1/build -I/tmp/src/chap-version_0_9_1/include -O3 -DNDEBUG -std=c++11 -o CMakeFiles/chap.dir/src/geometry/spline_curve_1D.cpp.o -c /tmp/src/chap-version_0_9_1/src/geometry/spline_curve_1D.cpp
/tmp/src/chap-version_0_9_1/src/geometry/spline_curve_1D.cpp:28:10: fatal error: boost/math/tools/minima.hpp: No such file or directory
#include <boost/math/tools/minima.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
CMakeFiles/chap.dir/build.make:398: recipe for target 'CMakeFiles/chap.dir/src/geometry/spline_curve_1D.cpp.o' failed
make[2]: *** [CMakeFiles/chap.dir/src/geometry/spline_curve_1D.cpp.o] Error 1
make[2]: Leaving directory '/tmp/src/chap-version_0_9_1/build'
CMakeFiles/Makefile2:355: recipe for target 'CMakeFiles/chap.dir/all' failed
make[1]: *** [CMakeFiles/chap.dir/all] Error 2
make[1]: Leaving directory '/tmp/src/chap-version_0_9_1/build'
Makefile:140: recipe for target 'all' failed
make: *** [all] Error 2
CMakeCache.txt is attached
CMakeCache.txt
Compiling chap on Ubuntu 16.04 LTS cmake seems to pass all of the tests: compiler working, found GROMACS, etc.
When I issue the make command, I get:
[ 10%] Building CXX object CMakeFiles/chap.dir/src/io/pdb_io.cpp.o
In file included from /home/winsvern2/Downloads/CHAP2/chap-version_0_9_1/src/io/pdb_io.cpp:31:0:
/home/winsvern2/Downloads/CHAP2/chap-version_0_9_1/include/io/pdb_io.hpp:49:38: error: ‘TopologyInformation’ in namespace ‘gmx’ does not name a type
void fromTopology(const gmx::TopologyInformation &top);
^
/home/winsvern2/Downloads/CHAP2/chap-version_0_9_1/src/io/pdb_io.cpp:40:20: error: ‘TopologyInformation’ in namespace ‘gmx’ does not name a type
const gmx::TopologyInformation &top)
^
/home/winsvern2/Downloads/CHAP2/chap-version_0_9_1/src/io/pdb_io.cpp: In member function ‘void PdbStructure::fromTopology(const int&)’:
/home/winsvern2/Downloads/CHAP2/chap-version_0_9_1/src/io/pdb_io.cpp:43:9: error: request for member ‘getTopologyConf’ in ‘top’, which is of non-class type ‘const int’
top.getTopologyConf(&coords_, box_);
^
/home/winsvern2/Downloads/CHAP2/chap-version_0_9_1/src/io/pdb_io.cpp:46:29: error: request for member ‘topology’ in ‘top’, which is of non-class type ‘const int’
t_topology *topol = top.topology();
^
/home/winsvern2/Downloads/CHAP2/chap-version_0_9_1/src/io/pdb_io.cpp:50:17: error: request for member ‘ePBC’ in ‘top’, which is of non-class type ‘const int’
ePBC_ = top.ePBC();
^
CMakeFiles/chap.dir/build.make:182: recipe for target 'CMakeFiles/chap.dir/src/io/pdb_io.cpp.o' failed
make[2]: *** [CMakeFiles/chap.dir/src/io/pdb_io.cpp.o] Error 1
CMakeFiles/Makefile2:392: recipe for target 'CMakeFiles/chap.dir/all' failed
make[1]: *** [CMakeFiles/chap.dir/all] Error 2
Makefile:138: recipe for target 'all' failed
make: *** [all] Error 2
I am sure the answer is simple, but my command of C++ is minimal. Thank you in advance for your help.
Hi
Here I want to make sure that can CHAP be used to analysis the pore produced in a pure bilayer system?
I built a DOPC bilayer system and exerted a electric field to produce a pore in it. Then I try to run CHAP to know how big the pore is, but failed. Following is what I did and got:
chap -f IRE_NPT_0.5.trr -s IRE_NPT_0.5_new.tpr
The Channel Annotation Package, version 0.9.1
Reading file IRE_NPT_0.5_new.tpr, VERSION 2018.8 (single precision)
Reading file IRE_NPT_0.5_new.tpr, VERSION 2018.8 (single precision)
Available static index groups:
Group 0 "System" (73918 atoms)
Group 1 "Other" (73918 atoms)
Group 2 "DOPC" (35328 atoms)
Group 3 "POT" (95 atoms)
Group 4 "CLA" (95 atoms)
Group 5 "TIP3" (38400 atoms)
Specify a selection for option 'sel-pathway'
(Reference group that defines the permeation pathway (usually 'Protein') ):
(one per line, for status/groups, 'help' for help)
2
Selection '2' parsed
trr version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Program: chap, version 2018.8
Standard library runtime error (possible bug):
(exception type: St13runtime_error)
No hydrophobicity scale data found for residue DOPC and no fallback specified.
Does it mean I need add the hydrophobicity scale data for DOPC manually?
How can I solve it?
Thanks a lot!
Hello,
I am running heuristic prediction for the example/example-03/ for the 6mhs.pdb. When I run ./heuristic_prediction.R I get the following error:
divide <- ggplot_build(mapped)[[1]][[1]]
Warning message:
Computation failed instat_contour()
:
Number of x coordinates must match number of columns in density matrix.
matrix <- matrix(c(divide$x, divide$y), ncol = 2)
Error in matrix(c(divide$x, divide$y), ncol = 2) :
'data' must be of a vector type, was 'NULL'
Execution halted
I am not familiar with R and hence I will be grateful if you could help me here.
Thanks.
Koushik
Hello,
After running chap and selecting water to analyze, I created the free energy profile, hydrophobicity profile, radius profile and solvent number density profile graphs from here:
https://www.channotation.org/docs/plotting_python/
The free energy profile and radius profile graphs look realistic.
The hydrophobicity profile graph is a straight line at 0. There are no dots on the graph to show the hydrophobicity profile. Do you know why the hydrophobicities are not being read?
The solvent number density profile graph for water contains consistent density around ~5-10 nm^-3. However, the pore being analyzed is huge (3-4 nm wide) so I would assume there is a free passage of water through the pore, and that the density should be closer to free water density (~33 nm^-3). Do you know why the solvent density would be lower than free water? Is this realistic?
Thanks for your help!
Hello,
I am wanting to use CHAP with my system, which contains several putative ion channels. What is the best way to go about this? From reading the documentation, I can think of a few ideas:
-pf-init-probe-pos
to be over each ion channelWhat would you recommend? This is a huge system, is why I'm asking for your recommendations instead of trying each of these. Thanks in advance!
Best,
Christian
chap -f 7_4.xtc -s new.tpr
CCCCCC HH HH AAA PPPPPPPP
CC CC HH HH AA AA PP PP
CC HH HH AA AA PP PP
CC HHHHHHHHH AA AA PPPPPPPP
CC HH HH AAAAAAAAA PP
CC CC HH HH AA AA PP
CCCCCC HH HH AA AA PP
The Channel Annotation Package, version 0.9.1
Reading file new.tpr, VERSION 2018 (single precision)
Reading file new.tpr, VERSION 2018 (single precision)
Available static index groups:
Group 0 "System" (47651 atoms)
Group 1 "Protein" (3533 atoms)
Group 2 "Protein-H" (1752 atoms)
Group 3 "C-alpha" (236 atoms)
Group 4 "Backbone" (708 atoms)
Group 5 "MainChain" (944 atoms)
Group 6 "MainChain+Cb" (1148 atoms)
Group 7 "MainChain+H" (1169 atoms)
Group 8 "SideChain" (2364 atoms)
Group 9 "SideChain-H" (808 atoms)
Group 10 "Prot-Masses" (3533 atoms)
Group 11 "non-Protein" (44118 atoms)
Group 12 "Other" (44118 atoms)
Group 13 "POPC" (17420 atoms)
Group 14 "POT" (23 atoms)
Group 15 "CLA" (26 atoms)
Group 16 "TIP3" (26649 atoms)
Specify a selection for option 'sel-pathway'
(Reference group that defines the permeation pathway (usually 'Protein') ):
(one per line, for status/groups, 'help' for help)
1
Selection '1' parsed
Program: chap, version 2018
Standard library runtime error (possible bug):
(exception type: St13runtime_error)
Pore radius at initial probe position is infinite. Consider increasing the
maximum pore radius with -pf-max-free-dist or set an appropriate cutoff for
neighbourhood searches explicitly with -pf-cutoff.
Thank you for using CHAP - The Channel Annotation Package!
Can CHAP read trajectory files other than gromacs like namd or desmond files?
Hi,
I can't figure out how to set the "-pf-init-probe-pos". I tried to get the coordinates from chimera, but I keep getting either:
Reading frames from pdb fileWARNING: all CONECT records are ignored
Reading frame 0 time -1.000 Segmentation fault
or
Pore radius at initial probe position is infinite. Consider increasing the
maximum pore radius with -pf-max-free-dist or set an appropriate cutoff for
neighbourhood searches explicitly with -pf-cutoff.
Maybe I get the coordinate position system wrong? Can you please let me know how to figure out what values put here?
Thanks,
Best,
Nicolas
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.