How to performed gmx_mmpbsa after performed gromacs from CHARMM_GUI website

[陳冠宇]

Dear sir,

I prepared the files from CHARMM_GUI website for doing MD simulation. (Setting list, amber ff19sb force field, OPC water model, gaff2)

However, I do not know how to operate gmx_mmpbsa after MD simulation (I had successfully finished the production procedure of MD). It seems to have some differences different from previous or traditional operations. For example, the index.ndx file is not the same as the previous format.

I try to do gmx_mmpbsa, but I meet some problems as below.  What can I do to fix the error?

Looking forward to hearing from you soon.

Thank you.

Mark, Guan-Yu Chen

"[INFO   ] Normal Complex: Saving group 1_13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb

[ERROR  ] MMPBSA_Error /usr/local/gromacs202201/bin/gmx trjconv failed when querying analysis.xtc.
           Check the gmx_MMPBSA.log file to report the problem.
  File "/home/markchen/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/markchen/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.make_prmtops()
  File "/home/markchen/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 537, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/markchen/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 116, in buildTopology
    self.gmx2pdb()
  File "/home/markchen/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 260, in gmx2pdb
    GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
  File "/home/markchen/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
    raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: /usr/local/gromacs202201/bin/gmx trjconv failed when querying analysis.xtc
Check the gmx_MMPBSA.log file to report the problem.
Error occurred on rank 0.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

"

[Mario Sergio Valdes]

You must follow the same procedure as always. You just need to make sure that you define the groups correctly. As far as I see you are defining groups 1 and 13, and that index.ndx does not have the same structure. Well, check your index.ndx (gmx make_ndx -f md.tpr -n index.ndx) and generate/locate the groups according to your system. You can see this example with an index.ndx generated by CHARMM-GUI (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Protein_ligand_CHARMMff/)

[陳冠宇]

Dear sir, 

Thank you for replying.

These problems seem to be solved. Attached is the log file.

However, I would like to share with you how I do it and to know whether it is correct or not.

I try to re-generate a new index.ndx file by this command: gmx make_ndx -f step5_1.gro -o new_index.ndx.

This command line changes the old index.ndx obtained from CHARMM-GUI to the new one. The old one only contained group (SOLU), group 1 (SOLV), group2 (System).

After carrying on the command, the new index contained two groups. One is a protein (ID: 1), and the other is a ligand (ID: 13). 

Subsequently, I use the command line: gmx trjconv -s step5_1.tpr -f step5_1.xtc -o analysis.xtc -pbc mol -ur compact

to remove PBC and obtain a new xtc file.

Next, perform the gmx_mmpbsa:mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs step5_1.tpr -ci new_index.ndx -cg 1 13 -ct analysis.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -do FINAL_DECOMP_MMPBSA.dat -eo FINAL_RESULTS_MM

PBSA.csv -deo FINAL_ENERGY_RESIDUE.csv -nogui

Looking forward to hearing from you soon

Thank you very much

Sincerely,

Mark, Guan-Yu Chen

感謝您

     

冠宇 敬上

***********************************

Mark, Guan-Yu Chen (陳冠宇) 

中國醫藥大學附設醫院 1JG1醫研部中醫藥研究發展中心

China Medicine Research and Development Center

China Medical University Hospital

Taiwan

Tel: +886-4-22053366 ext. 3316/5711

E-mail: markchen19822001(at)gmail.com 

E-mail: markchen19822001(at)yahoo.com.tw

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Mario Sergio Valdes <mariosergi...@gmail.com> 於 2022年11月4日 週五 晚上11:08寫道：

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[Mario Sergio Valdes]

Yes, it is perfectly fine. Generating a new index from the tpr is the most sensible option because all the molecules are already separated by groups.
The log file contains an error, you mistyped the command line. Note that gmx_MMPBSA_ana is an analysis tool, not an interface to run the calculations.

Mario S.

[陳冠宇]

Dear Sir,

Thank you for your reply.

I have successfully started gmx_mmpbsa_ana interface and saw my short tested trajectory(1000ps) of MD job. However, now, I meet a new problem about lincs errors during MD running. I hope I can solve this problem.

Thank you for your assistance.

Sincerely,

MARK

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