[INFO ] Started
[INFO ] Loading and checking parameter files for compatibility...
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/zhangxin/anaconda3/envs/Bio/bin/cpptraj
[INFO ] tleap found! Using /home/zhangxin/anaconda3/envs/Bio/bin/tleap
[INFO ] parmchk2 found! Using /home/zhangxin/anaconda3/envs/Bio/bin/parmchk2
[INFO ] mmpbsa_py_energy found! Using /home/zhangxin/anaconda3/envs/Bio/bin/mmpbsa_py_energy
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/zhangxin/env/gmx2020.4/bin/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER Topologies from GROMACS files...
[INFO ] Checking if supported force fields exists in Amber data...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
:-) GROMACS - gmx make_ndx, 2020.4 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx make_ndx, version 2020.4
Executable: /home/zhangxin/env/gmx2020.4/bin/gmx
Data prefix: /home/zhangxin/env/gmx2020.4
Working dir: /home/zhangxin/ACS/gmx/interaction/Nb6/pbsa
Command line:
gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx
GROMACS reminds you: "Chance favors the prepared mind." (Louis Pasteur)
Going to read 1 old index file(s)
Counted atom numbers up to 350281 in index file
0 System : 350281 atoms
1 Protein : 10156 atoms
2 Protein-H : 5163 atoms
3 C-alpha : 660 atoms
4 Backbone : 1980 atoms
5 MainChain : 2643 atoms
6 MainChain+Cb : 3250 atoms
7 MainChain+H : 3272 atoms
8 SideChain : 6884 atoms
9 SideChain-H : 2520 atoms
10 Prot-Masses : 10156 atoms
11 non-Protein : 340125 atoms
12 Water : 340116 atoms
13 SOL : 340116 atoms
14 non-Water : 10165 atoms
15 Ion : 9 atoms
16 CL : 9 atoms
17 Water_and_ions : 340125 atoms
18 receptor : 2102 atoms
19 com : 12136 atoms
20 ligand : 10034 atoms
nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups
'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues
't': atom type '|': or 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
>
>
>
Copied index group 18 'GMXMMPBSA_REC'
Copied index group 20 'GMXMMPBSA_LIG'
Merged two groups with OR: 2102 10034 -> 12136
21 GMXMMPBSA_REC_GMXMMPBSA_LIG: 12136 atoms
>
[INFO ] Normal Complex: Saving group 18_20 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
:-) GROMACS - gmx editconf, 2020.4 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx editconf, version 2020.4
Executable: /home/zhangxin/env/gmx2020.4/bin/gmx
Data prefix: /home/zhangxin/env/gmx2020.4
Working dir: /home/zhangxin/ACS/gmx/interaction/Nb6/pbsa
Command line:
gmx editconf -f md_0_1.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx
Reading file md_0_1.tpr, VERSION 2020.4 (single precision)
Reading file md_0_1.tpr, VERSION 2020.4 (single precision)
Select a group for output:
Group 0 ( System) has 350281 elements
Group 1 ( Protein) has 10156 elements
Group 2 ( Protein-H) has 5163 elements
Group 3 ( C-alpha) has 660 elements
Group 4 ( Backbone) has 1980 elements
Group 5 ( MainChain) has 2643 elements
Group 6 ( MainChain+Cb) has 3250 elements
Group 7 ( MainChain+H) has 3272 elements
Group 8 ( SideChain) has 6884 elements
Group 9 ( SideChain-H) has 2520 elements
Group 10 ( Prot-Masses) has 10156 elements
Group 11 ( non-Protein) has 340125 elements
Group 12 ( Water) has 340116 elements
Group 13 ( SOL) has 340116 elements
Group 14 ( non-Water) has 10165 elements
Group 15 ( Ion) has 9 elements
Group 16 ( CL) has 9 elements
Group 17 ( Water_and_ions) has 340125 elements
Group 18 ( GMXMMPBSA_REC) has 2102 elements
Group 19 ( com) has 12136 elements
Group 20 ( GMXMMPBSA_LIG) has 10034 elements
Group 21 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 12136 elements
Select a group:
GROMACS reminds you: "Contemplating answers that could break my bonds." (Peter Hammill)
Note that major changes are planned in future for editconf, to improve usability and utility.
Read 350281 atoms
Volume: 3485.93 nm^3, corresponds to roughly 1568600 electrons
Velocities found
Selected 21: 'GMXMMPBSA_REC_GMXMMPBSA_LIG'
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Complex: Saving group 18 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
:-) GROMACS - gmx editconf, 2020.4 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx editconf, version 2020.4
Executable: /home/zhangxin/env/gmx2020.4/bin/gmx
Data prefix: /home/zhangxin/env/gmx2020.4
Working dir: /home/zhangxin/ACS/gmx/interaction/Nb6/pbsa
Command line:
gmx editconf -f md_0_1.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx
Reading file md_0_1.tpr, VERSION 2020.4 (single precision)
Reading file md_0_1.tpr, VERSION 2020.4 (single precision)
Select a group for output:
Group 0 ( System) has 350281 elements
Group 1 ( Protein) has 10156 elements
Group 2 ( Protein-H) has 5163 elements
Group 3 ( C-alpha) has 660 elements
Group 4 ( Backbone) has 1980 elements
Group 5 ( MainChain) has 2643 elements
Group 6 ( MainChain+Cb) has 3250 elements
Group 7 ( MainChain+H) has 3272 elements
Group 8 ( SideChain) has 6884 elements
Group 9 ( SideChain-H) has 2520 elements
Group 10 ( Prot-Masses) has 10156 elements
Group 11 ( non-Protein) has 340125 elements
Group 12 ( Water) has 340116 elements
Group 13 ( SOL) has 340116 elements
Group 14 ( non-Water) has 10165 elements
Group 15 ( Ion) has 9 elements
Group 16 ( CL) has 9 elements
Group 17 ( Water_and_ions) has 340125 elements
Group 18 ( GMXMMPBSA_REC) has 2102 elements
Group 19 ( com) has 12136 elements
Group 20 ( GMXMMPBSA_LIG) has 10034 elements
Group 21 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 12136 elements
Select a group:
GROMACS reminds you: "You could give Aristotle a tutorial. And you could thrill him to the core of his being. Such is the privilege of living after Newton, Darwin, Einstein, Planck, Watson, Crick and their colleagues." (Richard Dawkins)
Note that major changes are planned in future for editconf, to improve usability and utility.
Read 350281 atoms
Volume: 3485.93 nm^3, corresponds to roughly 1568600 electrons
Velocities found
Selected 18: 'GMXMMPBSA_REC'
[INFO ] No ligand structure file was defined. Using ST approach...
[INFO ] Using ligand structure from complex to generate AMBER topology
[INFO ] Normal ligand: Saving group 20 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
:-) GROMACS - gmx editconf, 2020.4 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx editconf, version 2020.4
Executable: /home/zhangxin/env/gmx2020.4/bin/gmx
Data prefix: /home/zhangxin/env/gmx2020.4
Working dir: /home/zhangxin/ACS/gmx/interaction/Nb6/pbsa
Command line:
gmx editconf -f md_0_1.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx
Reading file md_0_1.tpr, VERSION 2020.4 (single precision)
Reading file md_0_1.tpr, VERSION 2020.4 (single precision)
Select a group for output:
Group 0 ( System) has 350281 elements
Group 1 ( Protein) has 10156 elements
Group 2 ( Protein-H) has 5163 elements
Group 3 ( C-alpha) has 660 elements
Group 4 ( Backbone) has 1980 elements
Group 5 ( MainChain) has 2643 elements
Group 6 ( MainChain+Cb) has 3250 elements
Group 7 ( MainChain+H) has 3272 elements
Group 8 ( SideChain) has 6884 elements
Group 9 ( SideChain-H) has 2520 elements
Group 10 ( Prot-Masses) has 10156 elements
Group 11 ( non-Protein) has 340125 elements
Group 12 ( Water) has 340116 elements
Group 13 ( SOL) has 340116 elements
Group 14 ( non-Water) has 10165 elements
Group 15 ( Ion) has 9 elements
Group 16 ( CL) has 9 elements
Group 17 ( Water_and_ions) has 340125 elements
Group 18 ( GMXMMPBSA_REC) has 2102 elements
Group 19 ( com) has 12136 elements
Group 20 ( GMXMMPBSA_LIG) has 10034 elements
Group 21 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 12136 elements
Select a group:
GROMACS reminds you: "Still I had a lurking question. Would it not be better if one could really 'see' whether molecules as complicated as the sterols, or strychnine were just as experiment suggested?" (Dorothy Hodgkin)
Note that major changes are planned in future for editconf, to improve usability and utility.
Read 350281 atoms
Volume: 3485.93 nm^3, corresponds to roughly 1568600 electrons
Velocities found
Selected 20: 'GMXMMPBSA_LIG'
[INFO ] Generating AMBER Compatible PDB Files...
[INFO ] Building Tleap input files...
-I: Adding /home/zhangxin/anaconda3/envs/Bio/dat/leap/prep to search path.
-I: Adding /home/zhangxin/anaconda3/envs/Bio/dat/leap/lib to search path.
-I: Adding /home/zhangxin/anaconda3/envs/Bio/dat/leap/parm to search path.
-I: Adding /home/zhangxin/anaconda3/envs/Bio/dat/leap/cmd to search path.
-f: Source _GMXMMPBSA_leap.in.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./_GMXMMPBSA_leap.in
----- Source: /home/zhangxin/anaconda3/envs/Bio/dat/leap/cmd/oldff/leaprc.ff99SBildn
----- Source of /home/zhangxin/anaconda3/envs/Bio/dat/leap/cmd/oldff/leaprc.ff99SBildn done
Log file: ./leap.log
Loading parameters: /home/zhangxin/anaconda3/envs/Bio/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /home/zhangxin/anaconda3/envs/Bio/dat/leap/parm/frcmod.ff99SBildn
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling) + ILDN corrections
Loading library: /home/zhangxin/anaconda3/envs/Bio/dat/leap/lib/all_nucleic94.lib
Loading library: /home/zhangxin/anaconda3/envs/Bio/dat/leap/lib/all_amino94ildn.lib
Loading library: /home/zhangxin/anaconda3/envs/Bio/dat/leap/lib/all_aminoct94ildn.lib
Loading library: /home/zhangxin/anaconda3/envs/Bio/dat/leap/lib/all_aminont94ildn.lib
Loading library: /home/zhangxin/anaconda3/envs/Bio/dat/leap/lib/ions94.lib
Loading library: /home/zhangxin/anaconda3/envs/Bio/dat/leap/lib/solvents.lib
----- Source: /home/zhangxin/anaconda3/envs/Bio/dat/leap/cmd/leaprc.gaff
----- Source of /home/zhangxin/anaconda3/envs/Bio/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/zhangxin/anaconda3/envs/Bio/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
Loading library: /home/zhangxin/anaconda3/envs/Bio/dat/leap/lib/atomic_ions.lib
Loading parameters: /home/zhangxin/anaconda3/envs/Bio/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set)
Using H(N)-modified Bondi radii
Loading PDB file: ./_GMXMMPBSA_REC_F1.pdb
Added missing heavy atom: .R<CGLN 273>.A<OXT 18>
total atoms in file: 16
Leap added 20 missing atoms according to residue templates:
1 Heavy
19 H / lone pairs
Loading PDB file: ./_GMXMMPBSA_REC_F2.pdb
Added missing heavy atom: .R<CLEU 274>.A<OXT 20>
total atoms in file: 8
Leap added 12 missing atoms according to residue templates:
1 Heavy
11 H / lone pairs
Loading PDB file: ./_GMXMMPBSA_REC_F3.pdb
Added missing heavy atom: .R<CSER 277>.A<OXT 12>
total atoms in file: 6
Leap added 6 missing atoms according to residue templates:
1 Heavy
5 H / lone pairs
Loading PDB file: ./_GMXMMPBSA_REC_F4.pdb
Added missing heavy atom: .R<CGLN 283>.A<OXT 18>
total atoms in file: 9
Leap added 9 missing atoms according to residue templates:
1 Heavy
8 H / lone pairs
Loading PDB file: ./_GMXMMPBSA_REC_F5.pdb
Added missing heavy atom: .R<CSER 295>.A<OXT 12>
total atoms in file: 6
Leap added 6 missing atoms according to residue templates:
1 Heavy
5 H / lone pairs
Loading PDB file: ./_GMXMMPBSA_REC_F6.pdb
Added missing heavy atom: .R<CGLY 320>.A<OXT 8>
total atoms in file: 9
Leap added 11 missing atoms according to residue templates:
1 Heavy
10 H / lone pairs
Loading PDB file: ./_GMXMMPBSA_REC_F7.pdb
Added missing heavy atom: .R<CALA 368>.A<OXT 11>
total atoms in file: 5
Leap added 6 missing atoms according to residue templates:
1 Heavy
5 H / lone pairs
Loading PDB file: ./_GMXMMPBSA_REC_F8.pdb
/home/zhangxin/anaconda3/envs/Bio/bin/teLeap: Warning!
Unknown residue: SOL number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
/home/zhangxin/anaconda3/envs/Bio/bin/teLeap: Warning!
-no luck
Creating new UNIT for residue: SOL sequence: 347
Created a new atom named: OW within residue: .R<SOL 347>
total atoms in file: 1
The file contained 1 atoms not in residue templates
Loading PDB file: ./_GMXMMPBSA_REC_F9.pdb
/home/zhangxin/anaconda3/envs/Bio/bin/teLeap: Fatal Error!
No atoms!
Exiting LEaP: Errors = 1; Warnings = 2; Notes = 0.
[ERROR ] /home/zhangxin/anaconda3/envs/Bio/bin/tleap failed when querying _GMXMMPBSA_leap.in