Error in including waters as a part of Receptor in gm_MMGBSA calculation

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Nazmul Hasan

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Jul 3, 2024, 3:48:24 PM (3 days ago) Jul 3

to gmx_MMPBSA

Hi All,

I am trying to reproduce the Nwat-GBSA protocol in Gromacs that the authors mentioned here in this article :

https://pubs.acs.org/doi/full/10.1021/acs.jcim.6b00196

The authors used AMBER for the calculation of GBSA while I am trying to reproduce it in Gromacs. I have made index group of Receptor with water (Receptor atoms and some closest water molecules) and Ligand and started gmx_MMGBSA calculation.

Now, I have got this error

gmx_MMPBSA does not support water/ions molecules in any structure, but we found 30 molecules in the complex.

I am attaching the log file here.

[INFO ] Starting gmx_MMPBSA v1.6.2
[DEBUG ] WDIR : /tank/data/LS/1ay7/original/ambf
[DEBUG ] AMBERHOME : /tank/data/LS/conda/envs/gmx_mmpbsa23
[DEBUG ] PYTHON EXE : /tank/data/LS/conda/envs/gmx_mmpbsa23/bin/python
[DEBUG ] PYTHON VERSION: 3.9.15 | packaged by conda-forge | (main, Nov 22 2022, 08:45:29) [GCC 10.4.0]
[DEBUG ] MPI : /sharedapps/spack/opt/spack/linux-rhel8-zen2/gcc-9.5.0/openmpi-4.1.3-avmeqoqdnqt7jmaxkpbcfsxf3opprwuk/bin/mpirun
[DEBUG ] ParmEd : 3.4.3+11.g41cc9ab
[DEBUG ] OS PLATFORM : Linux-4.18.0-513.24.1.el8_9.x86_64-x86_64-with-glibc2.28
[DEBUG ] OS SYSTEM : Linux
[DEBUG ] OS VERSION : #1 SMP Thu Mar 14 14:20:09 EDT 2024
[DEBUG ] OS PROCESSOR : x86_64

[INFO ] Command-line
gmx_MMPBSA -O -i mmgbsa.in -cp topol.top -cs md.tpr -ci index.ndx -cg 17 18 -ct md_center.xtc -o mmgbsares.dat -eo mmgbsares.csv

[DEBUG ] |Input file:
[DEBUG ] |--------------------------------------------------------------
[DEBUG ] |Sample input file for GB calculation
[DEBUG ] |#This input file is meant to show only that gmx_MMPBSA works. Although, we tried to use the input files as recommended in the
[DEBUG ] |#Amber manual, some parameters have been changed to perform more expensive calculations in a reasonable amount of time. Feel free to change the parameters
[DEBUG ] |#according to what is better for your system.
[DEBUG ] |
[DEBUG ] |&general
[DEBUG ] |sys_name="Prot-Prot",
[DEBUG ] |startframe=1102,
[DEBUG ] |endframe=1201,
[DEBUG ] |interval = 1
[DEBUG ] |forcefields="leaprc.protein.ff14SB",
[DEBUG ] |PBRadii=4,
[DEBUG ] |/
[DEBUG ] |&gb
[DEBUG ] |igb=8, saltcon=0.150,
[DEBUG ] |/
[DEBUG ] |--------------------------------------------------------------
[DEBUG ]
[INFO ] Checking mmgbsa.in input file...
[INFO ] Checking mmgbsa.in input file...Done.

[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /tank/data/LS/conda/envs/gmx_mmpbsa23/bin/cpptraj
[INFO ] tleap found! Using /tank/data/LS/conda/envs/gmx_mmpbsa23/bin/tleap
[INFO ] parmchk2 found! Using /tank/data/LS/conda/envs/gmx_mmpbsa23/bin/parmchk2
[INFO ] sander found! Using /tank/data/LS/conda/envs/gmx_mmpbsa23/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /sharedapps/spack/opt/spack/linux-rhel8-zen2/gcc-9.5.0/gromacs-2023-ihdgyftcl7cw7dioevipdadksccumpgs/bin/gmx
[INFO ] Checking external programs...Done.

[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[DEBUG ] Running command: echo -e "name 14 GMXMMPBSA_REC\n name 15 GMXMMPBSA_LIG\n 14 | 15\n q\n" | /sharedapps/spack/opt/spack/linux-rhel8-zen2/gcc-9.5.0/gromacs-2023-ihdgyftcl7cw7dioevipdadksccumpgs/bin/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f md.tpr
[DEBUG ] :-) GROMACS - gmx make_ndx, 2023 (-:
[DEBUG ]
[DEBUG ] Executable: /sharedapps/spack/opt/spack/linux-rhel8-zen2/gcc-9.5.0/gromacs-2023-ihdgyftcl7cw7dioevipdadksccumpgs/bin/gmx
[DEBUG ] Data prefix: /sharedapps/spack/opt/spack/linux-rhel8-zen2/gcc-9.5.0/gromacs-2023-ihdgyftcl7cw7dioevipdadksccumpgs
[DEBUG ] Working dir: /tank/data/LS/1ay7/original/ambf
[DEBUG ] Command line:
[DEBUG ] gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f md.tpr
[DEBUG ]
[DEBUG ]
[DEBUG ] Reading structure file
[DEBUG ] Reading file md.tpr, VERSION 2023 (single precision)
[DEBUG ] Reading file md.tpr, VERSION 2023 (single precision)
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Look at these, my work-strong arms" (P.J. Harvey)
[DEBUG ]
[DEBUG ] Going to read 1 old index file(s)
[DEBUG ]
[DEBUG ] 0 System : 2965 atoms
[DEBUG ] 1 Protein : 2875 atoms
[DEBUG ] 2 Protein-H : 1466 atoms
[DEBUG ] 3 C-alpha : 185 atoms
[DEBUG ] 4 Backbone : 555 atoms
[DEBUG ] 5 MainChain : 742 atoms
[DEBUG ] 6 MainChain+Cb : 914 atoms
[DEBUG ] 7 MainChain+H : 923 atoms
[DEBUG ] 8 SideChain : 1952 atoms
[DEBUG ] 9 SideChain-H : 724 atoms
[DEBUG ] 10 Prot-Masses : 2875 atoms
[DEBUG ] 11 non-Protein : 90 atoms
[DEBUG ] 12 Other : 90 atoms
[DEBUG ] 13 WT1 : 90 atoms
[DEBUG ] 14 r_1-96_WT1 : 1531 atoms
[DEBUG ] 15 r_97-185 : 1434 atoms
[DEBUG ]
[DEBUG ] nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups
[DEBUG ] 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues
[DEBUG ] 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help
[DEBUG ] 'r': residue 'res' nr 'chain' char
[DEBUG ] "name": group 'case': case sensitive 'q': save and quit
[DEBUG ] 'ri': residue index
[DEBUG ]
[DEBUG ] >
[DEBUG ]
[DEBUG ] >
[DEBUG ]
[DEBUG ] >
[DEBUG ] Copied index group 14 'GMXMMPBSA_REC'
[DEBUG ] Copied index group 15 'GMXMMPBSA_LIG'
[DEBUG ] Merged two groups with OR: 1531 1434 -> 2965
[DEBUG ]
[DEBUG ] >
[INFO ] Normal Complex: Saving group r_1-96_WT1_r_97-185 (14_15) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /sharedapps/spack/opt/spack/linux-rhel8-zen2/gcc-9.5.0/gromacs-2023-ihdgyftcl7cw7dioevipdadksccumpgs/bin/gmx trjconv -f md_center.xtc -s md.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2023 (-:
[DEBUG ]
[DEBUG ] Executable: /sharedapps/spack/opt/spack/linux-rhel8-zen2/gcc-9.5.0/gromacs-2023-ihdgyftcl7cw7dioevipdadksccumpgs/bin/gmx
[DEBUG ] Data prefix: /sharedapps/spack/opt/spack/linux-rhel8-zen2/gcc-9.5.0/gromacs-2023-ihdgyftcl7cw7dioevipdadksccumpgs
[DEBUG ] Working dir: /tank/data/LS/1ay7/original/ambf
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f md_center.xtc -s md.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ]
[DEBUG ] Will write pdb: Protein data bank file
[DEBUG ] Reading file md.tpr, VERSION 2023 (single precision)
[DEBUG ] Reading file md.tpr, VERSION 2023 (single precision)
[DEBUG ] Group 0 ( System) has 2965 elements
[DEBUG ] Group 1 ( Protein) has 2875 elements
[DEBUG ] Group 2 ( Protein-H) has 1466 elements
[DEBUG ] Group 3 ( C-alpha) has 185 elements
[DEBUG ] Group 4 ( Backbone) has 555 elements
[DEBUG ] Group 5 ( MainChain) has 742 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 914 elements
[DEBUG ] Group 7 ( MainChain+H) has 923 elements
[DEBUG ] Group 8 ( SideChain) has 1952 elements
[DEBUG ] Group 9 ( SideChain-H) has 724 elements
[DEBUG ] Group 10 ( Prot-Masses) has 2875 elements
[DEBUG ] Group 11 ( non-Protein) has 90 elements
[DEBUG ] Group 12 ( Other) has 90 elements
[DEBUG ] Group 13 ( WT1) has 90 elements
[DEBUG ] Group 14 ( GMXMMPBSA_REC) has 1531 elements
[DEBUG ] Group 15 ( GMXMMPBSA_LIG) has 1434 elements
[DEBUG ] Group 16 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 2965 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of md_center.xtc is 0.001 (nm)
[DEBUG ]
Reading frame 1 time 10.000
[DEBUG ] Dumping frame at t= 0 ps
[DEBUG ] Last written: frame 0 time 0.000
[DEBUG ]
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Look at these, my work-strong arms" (P.J. Harvey)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 16: '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 Receptor: Saving group r_1-96_WT1 (14) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[DEBUG ] Running command: echo -e "14"| /sharedapps/spack/opt/spack/linux-rhel8-zen2/gcc-9.5.0/gromacs-2023-ihdgyftcl7cw7dioevipdadksccumpgs/bin/gmx trjconv -f md_center.xtc -s md.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2023 (-:
[DEBUG ]
[DEBUG ] Executable: /sharedapps/spack/opt/spack/linux-rhel8-zen2/gcc-9.5.0/gromacs-2023-ihdgyftcl7cw7dioevipdadksccumpgs/bin/gmx
[DEBUG ] Data prefix: /sharedapps/spack/opt/spack/linux-rhel8-zen2/gcc-9.5.0/gromacs-2023-ihdgyftcl7cw7dioevipdadksccumpgs
[DEBUG ] Working dir: /tank/data/LS/1ay7/original/ambf
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f md_center.xtc -s md.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ]
[DEBUG ] Will write pdb: Protein data bank file
[DEBUG ] Reading file md.tpr, VERSION 2023 (single precision)
[DEBUG ] Reading file md.tpr, VERSION 2023 (single precision)
[DEBUG ] Group 0 ( System) has 2965 elements
[DEBUG ] Group 1 ( Protein) has 2875 elements
[DEBUG ] Group 2 ( Protein-H) has 1466 elements
[DEBUG ] Group 3 ( C-alpha) has 185 elements
[DEBUG ] Group 4 ( Backbone) has 555 elements
[DEBUG ] Group 5 ( MainChain) has 742 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 914 elements
[DEBUG ] Group 7 ( MainChain+H) has 923 elements
[DEBUG ] Group 8 ( SideChain) has 1952 elements
[DEBUG ] Group 9 ( SideChain-H) has 724 elements
[DEBUG ] Group 10 ( Prot-Masses) has 2875 elements
[DEBUG ] Group 11 ( non-Protein) has 90 elements
[DEBUG ] Group 12 ( Other) has 90 elements
[DEBUG ] Group 13 ( WT1) has 90 elements
[DEBUG ] Group 14 ( GMXMMPBSA_REC) has 1531 elements
[DEBUG ] Group 15 ( GMXMMPBSA_LIG) has 1434 elements
[DEBUG ] Group 16 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 2965 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of md_center.xtc is 0.001 (nm)
[DEBUG ]
Reading frame 1 time 10.000
[DEBUG ] Dumping frame at t= 0 ps
[DEBUG ] Last written: frame 0 time 0.000
[DEBUG ]
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Look at these, my work-strong arms" (P.J. Harvey)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 14: '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 r_97-185 (15) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[DEBUG ] Running command: echo -e "15"| /sharedapps/spack/opt/spack/linux-rhel8-zen2/gcc-9.5.0/gromacs-2023-ihdgyftcl7cw7dioevipdadksccumpgs/bin/gmx trjconv -f md_center.xtc -s md.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2023 (-:
[DEBUG ]
[DEBUG ] Executable: /sharedapps/spack/opt/spack/linux-rhel8-zen2/gcc-9.5.0/gromacs-2023-ihdgyftcl7cw7dioevipdadksccumpgs/bin/gmx
[DEBUG ] Data prefix: /sharedapps/spack/opt/spack/linux-rhel8-zen2/gcc-9.5.0/gromacs-2023-ihdgyftcl7cw7dioevipdadksccumpgs
[DEBUG ] Working dir: /tank/data/LS/1ay7/original/ambf
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f md_center.xtc -s md.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ]
[DEBUG ] Will write pdb: Protein data bank file
[DEBUG ] Reading file md.tpr, VERSION 2023 (single precision)
[DEBUG ] Reading file md.tpr, VERSION 2023 (single precision)
[DEBUG ] Group 0 ( System) has 2965 elements
[DEBUG ] Group 1 ( Protein) has 2875 elements
[DEBUG ] Group 2 ( Protein-H) has 1466 elements
[DEBUG ] Group 3 ( C-alpha) has 185 elements
[DEBUG ] Group 4 ( Backbone) has 555 elements
[DEBUG ] Group 5 ( MainChain) has 742 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 914 elements
[DEBUG ] Group 7 ( MainChain+H) has 923 elements
[DEBUG ] Group 8 ( SideChain) has 1952 elements
[DEBUG ] Group 9 ( SideChain-H) has 724 elements
[DEBUG ] Group 10 ( Prot-Masses) has 2875 elements
[DEBUG ] Group 11 ( non-Protein) has 90 elements
[DEBUG ] Group 12 ( Other) has 90 elements
[DEBUG ] Group 13 ( WT1) has 90 elements
[DEBUG ] Group 14 ( GMXMMPBSA_REC) has 1531 elements
[DEBUG ] Group 15 ( GMXMMPBSA_LIG) has 1434 elements
[DEBUG ] Group 16 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 2965 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of md_center.xtc is 0.001 (nm)
[DEBUG ]
Reading frame 1 time 10.000
[DEBUG ] Dumping frame at t= 0 ps
[DEBUG ] Last written: frame 0 time 0.000
[DEBUG ]
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Look at these, my work-strong arms" (P.J. Harvey)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 15: 'GMXMMPBSA_LIG'
[ERROR ] MMPBSA_Error

gmx_MMPBSA does not support water/ions molecules in any structure, but we found 30 molecules in the complex.

Check the gmx_MMPBSA.log file to report the problem.

How can I include water molecules from the simulation as a part of the Receptor like the authors did? Thanks in advance.

marioe911116

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Jul 3, 2024, 3:52:34 PM (3 days ago) Jul 3

to gmx_MMPBSA

Unfortunately, gmx_MMPBSA does not support the inclusion of explicit water molecules in the calculation.

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