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Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
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Failed to generate parameters #115

Closed carltonbiotec closed 2 years ago

carltonbiotec commented 2 years ago

Hai,

I am getting this error /home/dextro/amber/amber20_src/bin/teLeap: Warning! The unperturbed charge of the unit (-1.000000) is not zero. FATAL: Atom .R<CASP 23>.A<O2 15> does not have a type. FATAL: Atom .R<CASP 23>.A<O1 14> does not have a type.

/home/dextro/amber/amber20_src/bin/teLeap: Fatal Error! Failed to generate parameters

Exiting LEaP: Errors = 1; Warnings = 1; Notes = 0.

Please let me know what has to be done

Steps to reproduce the behavior:

  1. protein peptide interaction

Additional context The gmx_MMPBSA.log file

[INFO ] Starting [INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs mdsim.tpr -ci index.ndx -cg 19 20 -ct mdsim_allframes.pdb

[WARNING] protein_forcefield and ligand_forcefield variables are deprecate since version 1.4.1 and will be remove in the next version. Please, use forcefield instead. [WARNING] entropy_seg variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use ie_segment instead. [INFO ] Checking external programs... [INFO ] cpptraj found! Using /home/dextro/amber/amber20_src/bin/cpptraj [INFO ] tleap found! Using /home/dextro/amber/amber20_src/bin/tleap [INFO ] parmchk2 found! Using /home/dextro/amber/amber20_src/bin/parmchk2 [INFO ] mmpbsa_py_energy found! Using /home/dextro/amber/amber20_src/bin/mmpbsa_py_energy [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /usr/bin/gmx [INFO ] Checking external programs...Done.

[INFO ] Building AMBER Topologies from GROMACS files... [INFO ] Checking gmxMMPBSA data folder exists in Amber data... [INFO ] Get PDB files from GROMACS structures files... [INFO ] Making gmx_MMPBSA index for complex... [INFO ] Normal Complex: Saving group 19_20 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [WARNING] You must define the ligand mol2 file (-lm) if ligand_forcefield is "leaprc.gaff" or "leaprc.gaff2". If the ligand is parametrized in Amber force fields ignore this warning [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 19 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb [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 [INFO ] Generating AMBER Compatible PDB Files... [INFO ] Building tleap input files... [ERROR ] MMPBSA_Error /home/dextro/amber/amber20_src/bin/tleap failed when querying _GMXMMPBSA_leap.in. Check the gmx_MMPBSA.log file to report the problem. m, 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 2020.1-Ubuntu-2020.1-1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/dextro/amber/amber20_src Command line: gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx

GROMACS reminds you: "It's Against the Rules" (Pulp Fiction)

Going to read 1 old index file(s) Counted atom numbers up to 88130 in index file

0 System : 88130 atoms 1 Protein : 10282 atoms 2 Protein-H : 8070 atoms 3 C-alpha : 1013 atoms 4 Backbone : 3039 atoms 5 MainChain : 4054 atoms 6 MainChain+Cb : 5010 atoms 7 MainChain+H : 5005 atoms 8 SideChain : 5277 atoms 9 SideChain-H : 4016 atoms 10 Prot-Masses : 10282 atoms 11 non-Protein : 77848 atoms 12 Water : 77700 atoms 13 SOL : 77700 atoms 14 non-Water : 10430 atoms 15 Ion : 148 atoms 16 NA : 83 atoms 17 CL : 65 atoms 18 Water_and_ions : 77848 atoms 19 r_1-1004 : 10178 atoms 20 r_1005-1013 : 104 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 19 'GMXMMPBSA_REC' Copied index group 20 'GMXMMPBSA_LIG' Merged two groups with OR: 10178 104 -> 10282

21 GMXMMPBSA_REC_GMXMMPBSA_LIG: 10282 atoms

:-) GROMACS - gmx editconf, 2020.1-Ubuntu-2020.1-1 (-:

                        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 2020.1-Ubuntu-2020.1-1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/dextro/amber/amber20_src Command line: gmx editconf -f mdsim.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx

Reading file mdsim.tpr, VERSION 2019.2 (single precision) Reading file mdsim.tpr, VERSION 2019.2 (single precision)

Select a group for output: Group 0 ( System) has 88130 elements Group 1 ( Protein) has 10282 elements Group 2 ( Protein-H) has 8070 elements Group 3 ( C-alpha) has 1013 elements Group 4 ( Backbone) has 3039 elements Group 5 ( MainChain) has 4054 elements Group 6 ( MainChain+Cb) has 5010 elements Group 7 ( MainChain+H) has 5005 elements Group 8 ( SideChain) has 5277 elements Group 9 ( SideChain-H) has 4016 elements Group 10 ( Prot-Masses) has 10282 elements Group 11 ( non-Protein) has 77848 elements Group 12 ( Water) has 77700 elements Group 13 ( SOL) has 77700 elements Group 14 ( non-Water) has 10430 elements Group 15 ( Ion) has 148 elements Group 16 ( NA) has 83 elements Group 17 ( CL) has 65 elements Group 18 ( Water_and_ions) has 77848 elements Group 19 ( GMXMMPBSA_REC) has 10178 elements Group 20 ( GMXMMPBSA_LIG) has 104 elements Group 21 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 10282 elements Select a group: GROMACS reminds you: "No, no, you're not thinking, you're just being logical." (Niels Bohr)

Note that major changes are planned in future for editconf, to improve usability and utility. Read 88130 atoms Volume: 713.709 nm^3, corresponds to roughly 321100 electrons Velocities found Selected 21: 'GMXMMPBSA_REC_GMXMMPBSA_LIG' :-) GROMACS - gmx editconf, 2020.1-Ubuntu-2020.1-1 (-:

                        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 2020.1-Ubuntu-2020.1-1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/dextro/amber/amber20_src Command line: gmx editconf -f mdsim.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx

Reading file mdsim.tpr, VERSION 2019.2 (single precision) Reading file mdsim.tpr, VERSION 2019.2 (single precision)

Select a group for output: Group 0 ( System) has 88130 elements Group 1 ( Protein) has 10282 elements Group 2 ( Protein-H) has 8070 elements Group 3 ( C-alpha) has 1013 elements Group 4 ( Backbone) has 3039 elements Group 5 ( MainChain) has 4054 elements Group 6 ( MainChain+Cb) has 5010 elements Group 7 ( MainChain+H) has 5005 elements Group 8 ( SideChain) has 5277 elements Group 9 ( SideChain-H) has 4016 elements Group 10 ( Prot-Masses) has 10282 elements Group 11 ( non-Protein) has 77848 elements Group 12 ( Water) has 77700 elements Group 13 ( SOL) has 77700 elements Group 14 ( non-Water) has 10430 elements Group 15 ( Ion) has 148 elements Group 16 ( NA) has 83 elements Group 17 ( CL) has 65 elements Group 18 ( Water_and_ions) has 77848 elements Group 19 ( GMXMMPBSA_REC) has 10178 elements Group 20 ( GMXMMPBSA_LIG) has 104 elements Group 21 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 10282 elements Select a group: GROMACS reminds you: "Let Me Do This" (Urban Dance Squad)

Note that major changes are planned in future for editconf, to improve usability and utility. Read 88130 atoms Volume: 713.709 nm^3, corresponds to roughly 321100 electrons Velocities found Selected 19: 'GMXMMPBSA_REC' :-) GROMACS - gmx editconf, 2020.1-Ubuntu-2020.1-1 (-:

                        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 2020.1-Ubuntu-2020.1-1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/dextro/amber/amber20_src Command line: gmx editconf -f mdsim.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx

Reading file mdsim.tpr, VERSION 2019.2 (single precision) Reading file mdsim.tpr, VERSION 2019.2 (single precision)

Select a group for output: Group 0 ( System) has 88130 elements Group 1 ( Protein) has 10282 elements Group 2 ( Protein-H) has 8070 elements Group 3 ( C-alpha) has 1013 elements Group 4 ( Backbone) has 3039 elements Group 5 ( MainChain) has 4054 elements Group 6 ( MainChain+Cb) has 5010 elements Group 7 ( MainChain+H) has 5005 elements Group 8 ( SideChain) has 5277 elements Group 9 ( SideChain-H) has 4016 elements Group 10 ( Prot-Masses) has 10282 elements Group 11 ( non-Protein) has 77848 elements Group 12 ( Water) has 77700 elements Group 13 ( SOL) has 77700 elements Group 14 ( non-Water) has 10430 elements Group 15 ( Ion) has 148 elements Group 16 ( NA) has 83 elements Group 17 ( CL) has 65 elements Group 18 ( Water_and_ions) has 77848 elements Group 19 ( GMXMMPBSA_REC) has 10178 elements Group 20 ( GMXMMPBSA_LIG) has 104 elements Group 21 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 10282 elements Select a group: GROMACS reminds you: "I ought to warn you, I have no faith" (Jane Eyre in Jane Eyre by Charlotte Bronte)

Note that major changes are planned in future for editconf, to improve usability and utility. Read 88130 atoms Volume: 713.709 nm^3, corresponds to roughly 321100 electrons Velocities found Selected 20: 'GMXMMPBSA_LIG' -I: Adding /home/dextro/amber/amber20_src/dat/leap/prep to search path. -I: Adding /home/dextro/amber/amber20_src/dat/leap/lib to search path. -I: Adding /home/dextro/amber/amber20_src/dat/leap/parm to search path. -I: Adding /home/dextro/amber/amber20_src/dat/leap/cmd to search path. -f: Source _GMXMMPBSA_leap.in. -I: Adding /home/dextro/.local/lib/python3.8/site-packages/GMXMMPBSA/data to search path.

Welcome to LEaP! (no leaprc in search path) Sourcing: ./_GMXMMPBSA_leap.in ----- Source: /home/dextro/amber/amber20_src/dat/leap/cmd/oldff/leaprc.ff99SB ----- Source of /home/dextro/amber/amber20_src/dat/leap/cmd/oldff/leaprc.ff99SB done Log file: ./leap.log Loading parameters: /home/dextro/amber/amber20_src/dat/leap/parm/parm99.dat Reading title: PARM99 for DNA,RNA,AA, organic molecules, Polariz.& LP incl.02/04/99 Loading parameters: /home/dextro/amber/amber20_src/dat/leap/parm/frcmod.ff99SB Reading force field modification type file (frcmod) Reading title: Modification/update of parm99.dat (Hornak & Simmerling) Loading library: /home/dextro/amber/amber20_src/dat/leap/lib/all_nucleic94.lib Loading library: /home/dextro/amber/amber20_src/dat/leap/lib/all_amino94.lib Loading library: /home/dextro/amber/amber20_src/dat/leap/lib/all_aminoct94.lib Loading library: /home/dextro/amber/amber20_src/dat/leap/lib/all_aminont94.lib Loading library: /home/dextro/amber/amber20_src/dat/leap/lib/ions94.lib Loading library: /home/dextro/amber/amber20_src/dat/leap/lib/solvents.lib ----- Source: /home/dextro/amber/amber20_src/dat/leap/cmd/leaprc.gaff ----- Source of /home/dextro/amber/amber20_src/dat/leap/cmd/leaprc.gaff done Log file: ./leap.log Loading parameters: /home/dextro/amber/amber20_src/dat/leap/parm/gaff.dat Reading title: AMBER General Force Field for organic molecules (Version 1.81, May 2017) Loading library: /home/dextro/amber/amber20_src/dat/leap/lib/atomic_ions.lib Loading parameters: /home/dextro/amber/amber20_src/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 Created a new atom named: O1 within residue: .R<CILE 1036> Created a new atom named: O2 within residue: .R<CILE 1036> Added missing heavy atom: .R<CILE 1036>.A<O 19> Added missing heavy atom: .R<CILE 1036>.A<OXT 20> total atoms in file: 7992 Leap added 7875 missing atoms according to residue templates: 2 Heavy 7873 H / lone pairs The file contained 2 atoms not in residue templates Loading PDB file: ./_GMXMMPBSA_LIG_F1.pdb Created a new atom named: O1 within residue: .R<CASP 23> Created a new atom named: O2 within residue: .R<CASP 23> Added missing heavy atom: .R<CASP 23>.A<O 12> Added missing heavy atom: .R<CASP 23>.A<OXT 13> total atoms in file: 78 Leap added 78 missing atoms according to residue templates: 2 Heavy 76 H / lone pairs The file contained 2 atoms not in residue templates Checking Unit.

/home/dextro/amber/amber20_src/bin/teLeap: Warning! The unperturbed charge of the unit (-1.000000) is not zero. FATAL: Atom .R<CASP 23>.A<O2 15> does not have a type. FATAL: Atom .R<CASP 23>.A<O1 14> does not have a type.

/home/dextro/amber/amber20_src/bin/teLeap: Fatal Error! Failed to generate parameters

Exiting LEaP: Errors = 1; Warnings = 1; Notes = 0.

Valdes-Tresanco-MS commented 2 years ago

With what force field did you parameterize your system?

carltonbiotec commented 2 years ago

; ; Created by: ; :-) GROMACS - gmx pdb2gmx, 2019 (-: ;
; Executable: /usr/local/gromacs/bin/gmx ; Data prefix: /usr/local/gromacs ;
; Command line: ; gmx pdb2gmx -f clean-Native.pdb -water tip4p -ignh ; Force field was read from the standard GROMACS share directory. ;

; Include forcefield parameters

include "gromos43a1.ff/forcefield.itp"

; Include chain topologies

include "topol_Protein_chain_A.itp"

include "topol_Protein_chain_B.itp"

; Include water topology

include "gromos43a1.ff/tip4p.itp"

ifdef POSRES_WATER

; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000

endif

; Include topology for ions

include "gromos43a1.ff/ions.itp"

[ system ] ; Name Protein in water

[ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 SOL 19425 NA 83 CL 65

Valdes-Tresanco-MS commented 2 years ago

Currently, gmx_MMPBSA only supports AMBER and CHARMM force fields. We are working to implement the calculation with APBS but it will be available for version 2.0, which may take a while yet.