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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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CHAMBER prmtops cannot be used with 3D-RISM #400

Closed debanjansen48 closed 1 year ago

debanjansen48 commented 1 year ago

My Question is...

I executed protein ligand MD simulation using Gromacs. Now i want to study water placement using 3DRISM. But it return following error "CHAMBER prmtops cannot be used with 3D-RISM". The detaild error can be found at the last of my question. From the google group I came to know presently it only works with chamber prmtop files. My question is how to convert input files in CHAMBER format? or how to update my protocol to execute 3DRISM experiments? if it only works than why it saying CHAMBER prmtops cannot be used ???

[INFO ] Loading and checking parameter files for compatibility... [ERROR ] MMPBSA_Error

CHAMBER prmtops cannot be used with 3D-RISM

Check the gmx_MMPBSA.log file to report the problem. File "/home/debanjan/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/home/debanjan/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 99, in gmxmmpbsa app.loadcheck_prmtops() File "/home/debanjan/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 726, in loadcheck_prmtops GMXMMPBSA_ERROR('CHAMBER prmtops cannot be used with 3D-RISM') File "/home/debanjan/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in init raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.') MMPBSA_Error:

CHAMBER prmtops cannot be used with 3D-RISM

Check the gmx_MMPBSA.log file to report the problem. Exiting. All files have been retained.

Valdes-Tresanco-MS commented 1 year ago

Charmm ff is not compatible with 3D-RISM, so you need to change the ff (Amber) to use gmx_MMPBSA to do the calculation.

debanjansen48 commented 1 year ago

I used charmmgui to prepare input using Amber force field. And run 10ns MD simulation used given protocol to execute 3D-RISM. but encountered by following protocol.

**Define a valid index group

Check the gmx_MMPBSA.log file to report the problem.**

File "/home/debanjan/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/home/debanjan/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa app.make_prmtops() File "/home/debanjan/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology() File "/home/debanjan/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology self.gmx2pdb() File "/home/debanjan/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 245, in gmx2pdb num_com_rec_group, str_com_rec_group = get_index_groups(self.FILES.complex_index, com_rec_group) File "/home/debanjan/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 381, in get_index_groups GMXMMPBSA_ERROR('Define a valid index group') File "/home/debanjan/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in init raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.') MMPBSA_Error:

Define a valid index group

Check the gmx_MMPBSA.log file to report the problem. Exiting. All files have been retained.

Valdes-Tresanco-MS commented 1 year ago

Please, attach the gmx_MMPBSA.log file

Valdes-Tresanco-MS commented 1 year ago

Closing this issue as the original question has been resolved.