Error in running command for gmx_MMPBSA

[Ketan Rohilla]

Hey,

I am getting the following error when running command for gmx_MMPBSA:

[INFO   ] Checking mmpbsa.in input file...
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /root/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /root/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /root/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /root/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/local/gromacs/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...
[INFO   ] Normal Complex: Saving group 18_19 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[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 18 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 19 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Checking the structures consistency...
[INFO   ]
[INFO   ] Using topology conversion. Setting radiopt = 0...
[INFO   ] Building Normal Complex Amber topology...
/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:769: GromacsWarning: bondtypes funct != 1; unknown functional
  warnings.warn('bondtypes funct != 1; unknown functional',
/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:769: GromacsWarning: bondtypes funct != 1; unknown functional
  warnings.warn('bondtypes funct != 1; unknown functional',
/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:782: GromacsWarning: angletypes funct != 1 or 5; unknown functional
  warnings.warn('angletypes funct != 1 or 5; unknown functional',
/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:782: GromacsWarning: angletypes funct != 1 or 5; unknown functional
  warnings.warn('angletypes funct != 1 or 5; unknown functional',
/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:782: GromacsWarning: angletypes funct != 1 or 5; unknown functional
  warnings.warn('angletypes funct != 1 or 5; unknown functional',
/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:782: GromacsWarning: angletypes funct != 1 or 5; unknown functional
  warnings.warn('angletypes funct != 1 or 5; unknown functional',
/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:500: GromacsWarning: bond funct != 1; unknown functional
  warnings.warn('bond funct != 1; unknown functional',
/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py:500: GromacsWarning: bond funct != 1; unknown functional
  warnings.warn('bond funct != 1; unknown functional',

[Mario Sergio Valdes]

Gromos FF is not supported yet

[Mario Ernesto]

For calculating the MM part in MM/PB(GB)SA method, it's recommended to use the same force field that was used in the MD simulation... In this case, although it can work, it's not a best practice to use opls FF to calculate the MM part when you used gromos FF to run the MD simulation...

Cheers!

On Fri, Jun 17, 2022, 1:10 PM Jasdeep Singh <jasde...@gmail.com> wrote:

There is an indirect way to use gmxMMPBSA for systems simulated using gromos FF's.

The trajectories from gromos simulations can be spliited into multiple pdbs (as per analysis requirements) and again converted to OPLSAA format using pdb2gmx module. The OPLSAA formatted pdbs can now be procesed by gmxMMPBSA. Thanks!

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[jasdeep singh]

I fully agree with you Mario. It would be best to employ same ff. Although, I was referring to a relative analysis, your suggestions holds true. 

Best