tsjerk / backward Goto Github PK

Hi, i am working with protein-DNA complex. and i have encountered the following error.

"Traceback (most recent call last):
File "backward.py", line 956, in
raise ValueError("Residue not found in mapping dictionary: %s\n"%resn)
ValueError: Residue not found in mapping dictionary: DC"

When missing Mapping folder you get:

Traceback (most recent call last):
  File "/coarse/mariatsanai/backmapping/ITIC_test1/2_backmapping/20_percent/backward.py", line 11, in <module>
    import Mapping
ImportError: No module named Mapping

A clearer error message could be probably implemented.

I'm bringing up here too an issue coming from the Martini forum:

I am surprised to see that although there is a random kick option backward.py -kick, it appears to be nullified on line 190 of backward.py:

if False and res not in solvent_stuff:

that will always fail and therefore disallow the random kicks on the next line:

x,y,z = kick(x,size),kick(y,size),kick(z,size)

Does anybody know why random kicks have been disallowed? It may also be useful to remove the command line option entirely vs. this particular method of avoiding wholesale random kicks.

Hi Users,

I am new to CG simulations. After going through the tutorials and available online materials, I have managed to run the simulations for a protein disorder region using Martini-v3. However, during the back mapping to the all-atom representation of the system, I faced the below-mentioned error:

Now executing...

../Backward-master/initram.sh -f em2.gro -o em2_charmm.gro -to charmm36 -p topol.top -sol W

GROMACS VERSION:
MPI: false
/home/satyajit/satyajit/mediator/alphafold/Backward-master/backward.py -f em2.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to charmm36 -solname W
Error reading charmm27 to martini mapping for DOPS (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/thr.gromos.map).
Error reading charmm36 to martini mapping for DOPS (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/thr.gromos.map).
Error reading slipids to martini mapping for DOPS (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/thr.gromos.map).
Error reading amber to martini mapping for DOPS (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/thr.gromos.map).
Error reading charmm36 to martini mapping for REYP (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ser.charmm36.map).
Error reading charmm27 to martini mapping for POPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/pope.gromos.map).
Error reading charmm36 to martini mapping for POPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/pope.gromos.map).
Error reading slipids to martini mapping for POPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/pope.gromos.map).
Error reading amber to martini mapping for POPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/pope.gromos.map).
Error reading charmm27 to martini mapping for DOPE (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ile.gromos.map).
Error reading charmm36 to martini mapping for DOPE (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ile.gromos.map).
Error reading slipids to martini mapping for DOPE (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ile.gromos.map).
Error reading amber to martini mapping for DOPE (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ile.gromos.map).
Error reading charmm27 to martini mapping for DOPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/cdl4m.gromos.map).
Error reading charmm36 to martini mapping for DOPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/cdl4m.gromos.map).
Error reading slipids to martini mapping for DOPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/cdl4m.gromos.map).
Error reading amber to martini mapping for DOPG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/cdl4m.gromos.map).
Error reading charmm to martini mapping for TOG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/leu.amber.map).
Error reading charmm36 to martini mapping for TOG (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/leu.amber.map).
Error reading charmm27 to martini mapping for TOCL2 (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ala.gromos.map).
Error reading charmm36 to martini mapping for TOCL2 (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ala.gromos.map).
Error reading slipids to martini mapping for TOCL2 (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ala.gromos.map).
Error reading amber to martini mapping for TOCL2 (file: /home/satyajit/satyajit/mediator/alphafold/Backward-master/Mapping/ala.gromos.map).
Residues defined for transformation from martini to charmm36:
dict_keys(['CYS', 'VAL', 'ASP', 'DOPS', 'TYR', 'TRP', 'DOPC', 'PRO', 'LEU', 'REYP', 'SER', 'GB3', 'Gb3', 'ALA', 'DPPC', 'ASN', 'POPG', 'CHOL', 'POPC', 'DOPE', 'POPS', 'THR', 'DOPG', 'DPPG', 'GLU', 'GLN', 'LYS', 'DMPC', 'HIS', 'GLY', 'TOG', 'ARG', 'PHE', 'ILE', 'MET', 'TOCL2', 'POPE'])
None
gmx grompp -f 1-EM.mdp -c 0-backward.gro -n backmapped.ndx -p backmapped.top -o 1-EM -maxwarn 2
:-) GROMACS - gmx grompp, 2023.4 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/satyajit/satyajit/mediator/alphafold/med1
Command line:
gmx grompp -f 1-EM.mdp -c 0-backward.gro -n backmapped.ndx -p backmapped.top -o 1-EM -maxwarn 2

Setting the LD random seed to 2127810943

Generated 689 of the 356590 non-bonded parameter combinations

Excluding 1 bonded neighbours molecule type 'molecule_0'

Excluding 1 bonded neighbours molecule type 'W'

ERROR 1 [file backmapped.top, line 14]:
No such moleculetype NA

Program: gmx grompp, version 2023.4
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 2556)

Fatal error:
There was 1 error in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at https://manual.gromacs.org/current/user-guide/run-time-errors.html

My command line input is: ../Backward-master/initram.sh -f em2.gro -o em2_charmm.gro -to charmm36 -p topol.top -sol W

Any help will be appreciated.

With regards,
Satyajit Khatua

Hello everyone,

After performing a CG Martini3 simulation, I wanted to re-atomize a snapshot of a trajectory frame for structural analysis. I've done this before using Martini2 but using the backward.py script on a Martini3 model results in multiple errors. The GROMACS energy minimization step within initram.sh results in a 'Segmentation fault' error and prevents the complete script execution. Any information to resolve this issue would be appreciated.

My command line input:
../bash initram.sh -f 644125ps.gro -o all_atom.gro -to charmm36 -p topol.top

Now executing...

initram.sh -f 644125ps.gro -o all_atom.gro -to charmm36 -p topol.top

GROMACS VERSION:
MPI: false
/mnt/c/users/julia/Desktop/Martini3_ex/backward.py -f 644125ps.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to charmm36 -solname SOL
Error reading charmm27 to martini mapping for ALA (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/ala.gromos.map).
Error reading charmm36 to martini mapping for ALA (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/ala.gromos.map).
Error reading charmm27 to martini mapping for DOPG (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/dops.charmm36.map).
Error reading charmm36 to martini mapping for DOPG (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/dops.charmm36.map).
Error reading slipids to martini mapping for DOPG (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/dops.charmm36.map).
Error reading amber to martini mapping for DOPG (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/dops.charmm36.map).
Error reading charmm27 to martini mapping for DOPS (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/DPG1.alex.map).
Error reading charmm36 to martini mapping for DOPS (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/DPG1.alex.map).
Error reading slipids to martini mapping for DOPS (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/DPG1.alex.map).
Error reading amber to martini mapping for DOPS (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/DPG1.alex.map).
Error reading charmm36 to martini mapping for REYP (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/sep.gromos.map).
Error reading charmm27 to martini mapping for TOCL2 (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/tog.charmm36.map).
Error reading charmm36 to martini mapping for TOCL2 (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/tog.charmm36.map).
Error reading slipids to martini mapping for TOCL2 (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/tog.charmm36.map).
Error reading amber to martini mapping for TOCL2 (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/tog.charmm36.map).
Error reading charmm to martini mapping for TOG (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/trehalose.gromos.map).
Error reading charmm36 to martini mapping for TOG (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/trehalose.gromos.map).
Error reading charmm27 to martini mapping for TRP (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/trp.gromos.map).
Error reading charmm36 to martini mapping for TRP (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/trp.gromos.map).
Error reading charmm27 to martini mapping for TYR (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/tyr.gromos.map).
Error reading charmm36 to martini mapping for TYR (file: /mnt/c/users/julia/Desktop/Martini3_ex/Mapping/tyr.gromos.map).
Residues defined for transformation from martini to charmm36:
dict_keys(['A', 'ALA', 'ARG', 'ASN', 'ASP', 'C', 'CHOL', 'CYS', 'DA', 'DAT3', 'DAT5', 'DC', 'DCT3', 'DCT5', 'DG', 'DGT3', 'DGT5', 'DMPC', 'DOPC', 'DOPE', 'DOPG', 'DOPS', 'DPPC', 'DPPG', 'DT', 'DTT3', 'DTT5', 'G', 'GB3', 'Gb3', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'POPC', 'POPE', 'POPG', 'POPS', 'PRO', 'REYP', 'SER', 'THR', 'TOCL2', 'TOG', 'TRP', 'TYR', 'U', 'VAL'])
None
gmx grompp -f 1-EM.mdp -c 0-backward.gro -n backmapped.ndx -p backmapped.top -o 1-EM -maxwarn 2
:-) GROMACS - gmx grompp, 2023 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /mnt/c/users/julia/Desktop/Martini3_ex
Command line:
gmx grompp -f 1-EM.mdp -c 0-backward.gro -n backmapped.ndx -p backmapped.top -o 1-EM -maxwarn 2

Setting the LD random seed to -1778651149

Generated 168 of the 1653 non-bonded parameter combinations

Excluding 3 bonded neighbours molecule type 'Protein_chain_A'

WARNING 1 [file backmapped.top, line 134786]:
The following macros were defined in the 'define' mdp field with the -D
prefix, but were not used in the topology:
FLEXIBLE
If you haven't made a spelling error, either use the macro you defined,
or don't define the macro

WARNING 2 [file backmapped.top, line 134786]:
The GROMOS force fields have been parametrized with a physically
incorrect multiple-time-stepping scheme for a twin-range cut-off. When
used with a single-range cut-off (or a correct Trotter
multiple-time-stepping scheme), physical properties, such as the density,
might differ from the intended values. Since there are researchers
actively working on validating GROMOS with modern integrators we have not
yet removed the GROMOS force fields, but you should be aware of these
issues and check if molecules in your system are affected before
proceeding. Further information is available at
https://gitlab.com/gromacs/gromacs/-/issues/2884, and a longer
explanation of our decision to remove physically incorrect algorithms can
be found at https://doi.org/10.26434/chemrxiv.11474583.v1 .

NOTE 1 [file backmapped.top, line 134786]:
System has non-zero total charge: 41.000000
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.

Number of degrees of freedom in T-Coupling group rest is 61308.00
The integrator does not provide a ensemble temperature, there is no system ensemble temperature

NOTE 2 [file 1-EM.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.

This run will generate roughly 2 Mb of data

There were 2 NOTEs

There were 2 WARNINGs

GROMACS reminds you: "Given enough eyeballs, all bugs are shallow." (Linus Torvalds, on the power of open source)

gmx mdrun -deffnm 1-EM -v -nt 1
:-) GROMACS - gmx mdrun, 2023 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /mnt/c/users/julia/Desktop/Martini3_ex
Command line:
gmx mdrun -deffnm 1-EM -v -nt 1

Reading file 1-EM.tpr, VERSION 2023 (single precision)
1 GPU selected for this run.
Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:
PP:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
Using 1 MPI thread
Using 1 OpenMP thread

NOTE: Thread affinity was not set.

Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 500
Step= 0, Dmax= 1.0e-01 nm, Epot= 4.85033e+08 Fmax= 7.11856e+10, atom= 188
Step= 1, Dmax= 1.0e-01 nm, Epot= 8.89150e+07 Fmax= 9.04316e+08, atom= 9084
Step= 2, Dmax= 1.2e-01 nm, Epot= 3.55622e+07 Fmax= 1.72705e+07, atom= 4724
Step= 3, Dmax= 1.4e-01 nm, Epot= 2.14980e+07 Fmax= 4.20497e+06, atom= 4724
Step= 4, Dmax= 1.7e-01 nm, Epot= 1.47371e+07 Fmax= 9.96984e+05, atom= 15542
Step= 5, Dmax= 2.1e-01 nm, Epot= 6.67723e+06 Fmax= 1.70267e+06, atom= 8418
Step= 7, Dmax= 1.2e-01 nm, Epot= 5.62722e+06 Fmax= 3.36881e+05, atom= 5412
Step= 8, Dmax= 1.5e-01 nm, Epot= 4.37037e+06 Fmax= 7.70512e+05, atom= 18134
Step= 9, Dmax= 1.8e-01 nm, Epot= 3.88358e+06 Fmax= 4.81046e+05, atom= 18134
Step= 10, Dmax= 2.1e-01 nm, Epot= 3.53590e+06 Fmax= 2.36912e+05, atom= 3816
Step= 11, Dmax= 2.6e-01 nm, Epot= 3.01119e+06 Fmax= 8.37772e+05, atom= 14128
Step= 12, Dmax= 3.1e-01 nm, Epot= 2.55729e+06 Fmax= 1.49341e+05, atom= 14128
Step= 14, Dmax= 1.9e-01 nm, Epot= 2.23174e+06 Fmax= 6.38624e+05, atom= 13283
Step= 15, Dmax= 2.2e-01 nm, Epot= 1.96398e+06 Fmax= 1.33484e+05, atom= 4029
Step= 17, Dmax= 1.3e-01 nm, Epot= 1.75396e+06 Fmax= 7.36521e+05, atom= 8263
Step= 18, Dmax= 1.6e-01 nm, Epot= 1.61242e+06 Fmax= 1.51815e+05, atom= 6301
Step= 19, Dmax= 1.9e-01 nm, Epot= 1.59207e+06 Fmax= 4.86167e+05, atom= 6303
Step= 20, Dmax= 2.3e-01 nm, Epot= 1.30992e+06 Fmax= 2.45264e+05, atom= 18105
Step= 22, Dmax= 1.4e-01 nm, Epot= 1.23323e+06 Fmax= 2.60334e+06, atom= 18110
Step= 23, Dmax= 1.7e-01 nm, Epot= 1.17183e+06 Fmax= 2.26053e+05, atom= 18109
Step= 24, Dmax= 2.0e-01 nm, Epot= 1.11470e+06 Fmax= 4.05429e+05, atom= 13032
Step= 25, Dmax= 2.4e-01 nm, Epot= 1.07217e+06 Fmax= 3.29393e+05, atom= 13032
Step= 26, Dmax= 2.9e-01 nm, Epot= 9.60050e+05 Fmax= 4.28212e+05, atom= 13030
Step= 28, Dmax= 1.7e-01 nm, Epot= 8.92822e+05 Fmax= 4.39478e+05, atom= 2271
Step= 29, Dmax= 2.1e-01 nm, Epot= 8.57860e+05 Fmax= 2.09576e+06, atom= 2271
Step= 30, Dmax= 2.5e-01 nm, Epot= 8.43528e+05 Fmax= 9.02032e+05, atom= 2263
Step= 31, Dmax= 3.0e-01 nm, Epot= 7.93643e+05 Fmax= 1.23980e+05, atom= 5925
Step= 34, Dmax= 8.9e-02 nm, Epot= 7.15279e+05 Fmax= 1.78590e+05, atom= 9033
Step= 36, Dmax= 5.4e-02 nm, Epot= 7.10623e+05 Fmax= 1.35118e+05, atom= 12581
Step= 37, Dmax= 6.4e-02 nm, Epot= 6.41132e+05 Fmax= 1.23469e+05, atom= 1670
Step= 40, Dmax= 1.9e-02 nm, Epot= 6.11483e+05 Fmax= 1.37938e+05, atom= 16709
Step= 41, Dmax= 2.3e-02 nm, Epot= 5.85667e+05 Fmax= 1.71870e+05, atom= 17458
Step= 42, Dmax= 2.8e-02 nm, Epot= 5.42215e+05 Fmax= 1.41299e+05, atom= 13406
Step= 44, Dmax= 1.7e-02 nm, Epot= 4.94227e+05 Fmax= 1.41570e+05, atom= 52436
Step= 46, Dmax= 1.0e-02 nm, Epot= 4.53111e+05 Fmax= 9.38372e+05, atom= 14130
Step= 47, Dmax= 1.2e-02 nm, Epot= 4.36512e+05 Fmax= 1.37887e+05, atom= 15970
Step= 50, Dmax= 3.6e-03 nm, Epot= 4.24298e+05 Fmax= 1.36315e+06, atom= 13408
Step= 51, Dmax= 4.3e-03 nm, Epot= 4.19848e+05 Fmax= 1.34886e+05, atom= 11693
Step= 53, Dmax= 2.6e-03 nm, Epot= 4.12426e+05 Fmax= 5.69385e+05, atom= 7164
Step= 54, Dmax= 3.1e-03 nm, Epot= 4.07180e+05 Fmax= 1.27546e+05, atom= 11776
Step= 57, Dmax= 9.3e-04 nm, Epot= 4.03964e+05 Fmax= 2.25327e+05, atom= 15972
Step= 58, Dmax= 1.1e-03 nm, Epot= 4.00012e+05 Fmax= 4.63011e+05, atom= 15973
Step= 59, Dmax= 1.3e-03 nm, Epot= 3.98764e+05 Fmax= 9.26642e+04, atom= 11946
Step= 63, Dmax= 2.0e-04 nm, Epot= 3.97455e+05 Fmax= 1.95939e+05, atom= 12370
Step= 64, Dmax= 2.4e-04 nm, Epot= 3.96943e+05 Fmax= 2.38277e+05, atom= 18383
Step= 65, Dmax= 2.9e-04 nm, Epot= 3.96496e+05 Fmax= 1.59611e+05, atom= 11778
Step= 67, Dmax= 1.7e-04 nm, Epot= 3.96012e+05 Fmax= 1.88325e+05, atom= 11778
Step= 68, Dmax= 2.1e-04 nm, Epot= 3.95800e+05 Fmax= 2.14286e+05, atom= 12369
Step= 69, Dmax= 2.5e-04 nm, Epot= 3.95536e+05 Fmax= 7.45955e+05, atom= 16954
initram.sh: line 372: 129 Segmentation fault $M
gmx grompp -f 2-EM.mdp -c 1-EM.gro -n backmapped.ndx -p backmapped.top -o 2-EM -maxwarn 2
:-) GROMACS - gmx grompp, 2023 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /mnt/c/users/julia/Desktop/Martini3_ex
Command line:
gmx grompp -f 2-EM.mdp -c 1-EM.gro -n backmapped.ndx -p backmapped.top -o 2-EM -maxwarn 2

Program: gmx grompp, version 2023
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 271)
Function: void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
In command-line option -c
File '1-EM.gro' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I think the logic was off: (initram.sh line 447-452 and 365-370)

if $MPI
then
NT=
else
NT="-nt $NP"
fi

I guess it should be:

if $MPI
then
NT="-nt $NP"
else
NT=
fi