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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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[Question]: MMPBSA_Error: Selecting residue A:GLY:76 can't be mutated. Please, define a valid residue... #431

Closed zengdashi closed 8 months ago

zengdashi commented 8 months ago

My Question is...

I can't selecting Proline and Glycine when I run Alanine scanning.

zengdashi commented 8 months ago

Here is the log file [INFO ] Starting gmx_MMPBSA v1.6.2 [DEBUG ] WDIR : /home/zengfuming/APP/project/F17A [DEBUG ] AMBERHOME : /home/zengfuming/miniconda/envs/gmxMMPBSA [DEBUG ] PYTHON EXE : /home/zengfuming/miniconda/envs/gmxMMPBSA/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 : /home/zengfuming/miniconda/envs/gmxMMPBSA/bin/mpirun [DEBUG ] ParmEd : 3.4.3+11.g41cc9ab [DEBUG ] OS PLATFORM : Linux-6.2.0-35-generic-x86_64-with-glibc2.35 [DEBUG ] OS SYSTEM : Linux [DEBUG ] OS VERSION : #35~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Oct 6 10:23:26 UTC 2 [DEBUG ] OS PROCESSOR : x86_64

[INFO ] Command-line gmx_MMPBSA -O -i mmpbsaP39A.in -cs com.tpr -ct com_traj.xtc -ci index.ndx -cg 1 13 -cp topol.top -cr com.pdb -o mmpbsaP39A/FINAL_RESULTS_MMPBSA.dat -eo mmpbsaP39A/FINAL_RESULTS_MMPBSA.csv

[DEBUG ] |Input file: [DEBUG ] |-------------------------------------------------------------- [DEBUG ] |This is an input file used to calculate the change in CLR free energy [DEBUG ] |after residues 17, 21, 39, 76, 116, 118, 127, 129 mutated into ALA [DEBUG ] | [DEBUG ] |&general [DEBUG ] | sys_name="ALA_SCANNING" [DEBUG ] | startframe=1000, [DEBUG ] | endframe=6000, [DEBUG ] | PBRadii=4, [DEBUG ] |/ [DEBUG ] |&gb [DEBUG ] | igb=8, saltcon=0.150, [DEBUG ] |/ [DEBUG ] |&alanine_scanning [DEBUG ] | mutant_res='A/39', [DEBUG ] | mutant='ALA', [DEBUG ] | cas_intdiel=1 [DEBUG ] |/ [DEBUG ] | [DEBUG ] |-------------------------------------------------------------- [DEBUG ] [INFO ] Checking mmpbsaP39A.in input file... [INFO ] Checking mmpbsaP39A.in input file...Done.

[INFO ] Checking external programs... [INFO ] cpptraj found! Using /home/zengfuming/miniconda/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /home/zengfuming/miniconda/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /home/zengfuming/miniconda/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /home/zengfuming/miniconda/envs/gmxMMPBSA/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /home/zengfuming/miniconda/envs/gmxMMPBSA/bin.AVX2_256/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 1 GMXMMPBSA_REC\n name 13 GMXMMPBSA_LIG\n 1 | 13\n q\n" | /home/zengfuming/miniconda/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f com.tpr [DEBUG ] :-) GROMACS - gmx make_ndx, 2022.4-conda_forge (-: [DEBUG ] [DEBUG ] Executable: /home/zengfuming/miniconda/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/zengfuming/miniconda/envs/gmxMMPBSA [DEBUG ] Working dir: /home/zengfuming/APP/project/F17A [DEBUG ] Command line: [DEBUG ] gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f com.tpr [DEBUG ] [DEBUG ] [DEBUG ] Reading structure file [DEBUG ] Reading file com.tpr, VERSION 2018.8 (single precision) [DEBUG ] Reading file com.tpr, VERSION 2018.8 (single precision) [DEBUG ] [DEBUG ] GROMACS reminds you: "UNIX is basically a simple operating system. It just takes a genius to understand its simplicity." (Dennis Ritchie) [DEBUG ] [DEBUG ] Going to read 1 old index file(s) [DEBUG ] [DEBUG ] 0 System : 25811 atoms [DEBUG ] 1 Protein : 2092 atoms [DEBUG ] 2 Protein-H : 1051 atoms [DEBUG ] 3 C-alpha : 134 atoms [DEBUG ] 4 Backbone : 402 atoms [DEBUG ] 5 MainChain : 537 atoms [DEBUG ] 6 MainChain+Cb : 661 atoms [DEBUG ] 7 MainChain+H : 672 atoms [DEBUG ] 8 SideChain : 1420 atoms [DEBUG ] 9 SideChain-H : 514 atoms [DEBUG ] 10 Prot-Masses : 2092 atoms [DEBUG ] 11 non-Protein : 23719 atoms [DEBUG ] 12 Other : 76 atoms [DEBUG ] 13 CLR : 76 atoms [DEBUG ] 14 NA : 3 atoms [DEBUG ] 15 Water : 23640 atoms [DEBUG ] 16 SOL : 23640 atoms [DEBUG ] 17 non-Water : 2171 atoms [DEBUG ] 18 Ion : 3 atoms [DEBUG ] 19 CLR : 76 atoms [DEBUG ] 20 NA : 3 atoms [DEBUG ] 21 Water_and_ions : 23643 atoms [DEBUG ] 22 Protein_CLR : 2168 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 1 'GMXMMPBSA_REC' [DEBUG ] Copied index group 13 'GMXMMPBSA_LIG' [DEBUG ] Merged two groups with OR: 2092 76 -> 2168 [DEBUG ] [DEBUG ] 23 GMXMMPBSA_REC_GMXMMPBSA_LIG: 2168 atoms [DEBUG ] [DEBUG ] > [INFO ] Normal Complex: Saving group Protein_CLR (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /home/zengfuming/miniconda/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2022.4-conda_forge (-: [DEBUG ] [DEBUG ] Executable: /home/zengfuming/miniconda/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/zengfuming/miniconda/envs/gmxMMPBSA [DEBUG ] Working dir: /home/zengfuming/APP/project/F17A [DEBUG ] Command line: [DEBUG ] gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file com.tpr, VERSION 2018.8 (single precision) [DEBUG ] Reading file com.tpr, VERSION 2018.8 (single precision) [DEBUG ] Group 0 ( System) has 25811 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 2092 elements [DEBUG ] Group 2 ( Protein-H) has 1051 elements [DEBUG ] Group 3 ( C-alpha) has 134 elements [DEBUG ] Group 4 ( Backbone) has 402 elements [DEBUG ] Group 5 ( MainChain) has 537 elements [DEBUG ] Group 6 ( MainChain+Cb) has 661 elements [DEBUG ] Group 7 ( MainChain+H) has 672 elements [DEBUG ] Group 8 ( SideChain) has 1420 elements [DEBUG ] Group 9 ( SideChain-H) has 514 elements [DEBUG ] Group 10 ( Prot-Masses) has 2092 elements [DEBUG ] Group 11 ( non-Protein) has 23719 elements [DEBUG ] Group 12 ( Other) has 76 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 76 elements [DEBUG ] Group 14 ( NA) has 3 elements [DEBUG ] Group 15 ( Water) has 23640 elements [DEBUG ] Group 16 ( SOL) has 23640 elements [DEBUG ] Group 17 ( non-Water) has 2171 elements [DEBUG ] Group 18 ( Ion) has 3 elements [DEBUG ] Group 19 ( CLR) has 76 elements [DEBUG ] Group 20 ( NA) has 3 elements [DEBUG ] Group 21 ( Water_and_ions) has 23643 elements [DEBUG ] Group 22 ( Protein_CLR) has 2168 elements [DEBUG ] Group 23 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 2168 elements Reading frame 0 time 0.000
[DEBUG ] Precision of com_traj.xtc is 0.001 (nm) Reading frame 1 time 30.000
[DEBUG ] Dumping frame at t= 0 ps [DEBUG ] Last written: frame 0 time 0.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "UNIX is basically a simple operating system. It just takes a genius to understand its simplicity." (Dennis Ritchie) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 23: '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 Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb [DEBUG ] Running command: echo -e "1"| /home/zengfuming/miniconda/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2022.4-conda_forge (-: [DEBUG ] [DEBUG ] Executable: /home/zengfuming/miniconda/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/zengfuming/miniconda/envs/gmxMMPBSA [DEBUG ] Working dir: /home/zengfuming/APP/project/F17A [DEBUG ] Command line: [DEBUG ] gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file com.tpr, VERSION 2018.8 (single precision) [DEBUG ] Reading file com.tpr, VERSION 2018.8 (single precision) [DEBUG ] Group 0 ( System) has 25811 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 2092 elements [DEBUG ] Group 2 ( Protein-H) has 1051 elements [DEBUG ] Group 3 ( C-alpha) has 134 elements [DEBUG ] Group 4 ( Backbone) has 402 elements [DEBUG ] Group 5 ( MainChain) has 537 elements [DEBUG ] Group 6 ( MainChain+Cb) has 661 elements [DEBUG ] Group 7 ( MainChain+H) has 672 elements [DEBUG ] Group 8 ( SideChain) has 1420 elements [DEBUG ] Group 9 ( SideChain-H) has 514 elements [DEBUG ] Group 10 ( Prot-Masses) has 2092 elements [DEBUG ] Group 11 ( non-Protein) has 23719 elements [DEBUG ] Group 12 ( Other) has 76 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 76 elements [DEBUG ] Group 14 ( NA) has 3 elements [DEBUG ] Group 15 ( Water) has 23640 elements [DEBUG ] Group 16 ( SOL) has 23640 elements [DEBUG ] Group 17 ( non-Water) has 2171 elements [DEBUG ] Group 18 ( Ion) has 3 elements [DEBUG ] Group 19 ( CLR) has 76 elements [DEBUG ] Group 20 ( NA) has 3 elements [DEBUG ] Group 21 ( Water_and_ions) has 23643 elements [DEBUG ] Group 22 ( Protein_CLR) has 2168 elements [DEBUG ] Group 23 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 2168 elements Reading frame 0 time 0.000
[DEBUG ] Precision of com_traj.xtc is 0.001 (nm) Reading frame 1 time 30.000
[DEBUG ] Dumping frame at t= 0 ps [DEBUG ] Last written: frame 0 time 0.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "UNIX is basically a simple operating system. It just takes a genius to understand its simplicity." (Dennis Ritchie) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 1: '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 CLR (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [DEBUG ] Running command: echo -e "13"| /home/zengfuming/miniconda/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2022.4-conda_forge (-: [DEBUG ] [DEBUG ] Executable: /home/zengfuming/miniconda/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/zengfuming/miniconda/envs/gmxMMPBSA [DEBUG ] Working dir: /home/zengfuming/APP/project/F17A [DEBUG ] Command line: [DEBUG ] gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file com.tpr, VERSION 2018.8 (single precision) [DEBUG ] Reading file com.tpr, VERSION 2018.8 (single precision) [DEBUG ] Group 0 ( System) has 25811 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 2092 elements [DEBUG ] Group 2 ( Protein-H) has 1051 elements [DEBUG ] Group 3 ( C-alpha) has 134 elements [DEBUG ] Group 4 ( Backbone) has 402 elements [DEBUG ] Group 5 ( MainChain) has 537 elements [DEBUG ] Group 6 ( MainChain+Cb) has 661 elements [DEBUG ] Group 7 ( MainChain+H) has 672 elements [DEBUG ] Group 8 ( SideChain) has 1420 elements [DEBUG ] Group 9 ( SideChain-H) has 514 elements [DEBUG ] Group 10 ( Prot-Masses) has 2092 elements [DEBUG ] Group 11 ( non-Protein) has 23719 elements [DEBUG ] Group 12 ( Other) has 76 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 76 elements [DEBUG ] Group 14 ( NA) has 3 elements [DEBUG ] Group 15 ( Water) has 23640 elements [DEBUG ] Group 16 ( SOL) has 23640 elements [DEBUG ] Group 17 ( non-Water) has 2171 elements [DEBUG ] Group 18 ( Ion) has 3 elements [DEBUG ] Group 19 ( CLR) has 76 elements [DEBUG ] Group 20 ( NA) has 3 elements [DEBUG ] Group 21 ( Water_and_ions) has 23643 elements [DEBUG ] Group 22 ( Protein_CLR) has 2168 elements [DEBUG ] Group 23 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 2168 elements Reading frame 0 time 0.000
[DEBUG ] Precision of com_traj.xtc is 0.001 (nm) Reading frame 1 time 30.000
[DEBUG ] Dumping frame at t= 0 ps [DEBUG ] Last written: frame 0 time 0.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "UNIX is basically a simple operating system. It just takes a genius to understand its simplicity." (Dennis Ritchie) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 13: 'GMXMMPBSA_LIG' [INFO ] Checking the structures consistency... [INFO ] Assigning chain ID to structures files according to the reference structure... [INFO ] [INFO ] Using topology conversion. Setting radiopt = 0... [INFO ] Building Normal Complex Amber topology... [INFO ] Detected Amber/OPLS force field topology format... [WARNING] 10 invalid DIHEDRAL_PERIODICITY = 0 found in Complex topology... Setting DIHEDRAL_PERIODICITY = 1 [INFO ] Assigning PBRadii mbondi3 to Complex... [INFO ] Writing Normal Complex AMBER topology... [INFO ] No Receptor topology file was defined. Using ST approach... [INFO ] Building AMBER Receptor topology from Complex... [INFO ] Assigning PBRadii mbondi3 to Receptor... [INFO ] Writing Normal Receptor AMBER topology... [INFO ] No Ligand topology file was defined. Using ST approach... [INFO ] Building AMBER Ligand topology from Complex... [INFO ] Assigning PBRadii mbondi3 to Ligand... [INFO ] Writing Normal Ligand AMBER topology... [INFO ] Building Mutant Complex Topology... [ERROR ] MMPBSA_Error

Selecting residue A:PRO:39 can't be mutated. Please, define a valid residue...

Check the gmx_MMPBSA.log file to report the problem.

I can select F,M,L,R,Y as mutant residue

marioernestovaldes commented 8 months ago

The built-in algorithm for mutating aminoacids doesn't support glycine or proline...

zengdashi commented 8 months ago

Are there any solution for this problem?

marioernestovaldes commented 8 months ago

Unfortunately, it can't be done using the built-in algo for alanine scanning... However, you could run the MD for those mutants and calculate the difference in energy. In order to ensure similarity with the alanine scanning algorithm, make sure to use position restraints in the MD simulations of the native and the mutants.

zengdashi commented 8 months ago

Thank you very much for your answer！I will try to run MD for these mutants