gmx_MMPBSA for desmond traj

[John]

Dear all,

Is it possible to use gmx_MMPBSA for desmond generated trajectories? I generated a pdb and .trr files using VMD and was able to get an index file from pdb. I have been trying different tweaks with no luck. The latest error I got is 

[INFO   ] Normal Ligand: Saving group 14 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Checking the structures consistency...
[INFO   ]
[ERROR  ] MMPBSA_Error The PBRadii charmm_radii is not compatible with Amber topologies....
           Check the gmx_MMPBSA.log file to report the problem.
  File "/home/alaooj/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/alaooj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/alaooj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 548, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/alaooj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 120, in buildTopology
    self.pdb2prmtop()
  File "/home/alaooj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 675, in pdb2prmtop
    GMXMMPBSA_ERROR(f"The PBRadii {PBRadii[self.INPUT['PBRadii']]} is not compatible with Amber topologies...")
  File "/home/alaooj/anaconda3/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: The PBRadii charmm_radii is not compatible with Amber topologies...
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

Thanks.

[Mario Sergio Valdes]

At the moment, we do not have support for desmond, we have not tested it yet. In this case, the error is because you are using charmm_radii, which is not compatible with the AMBER force field. Even if you have used another forcefield in desmond, when using a PDB and not defining -cp topol.top, the topology is built with tLeap, which assumes that the forcefield is the one defined in the forcefields variable. This may conflict with the radii you are selecting and even create artificial results. You must be careful

[Mario Sergio Valdes]

Thanks Mario.
I was contemplating using it because I was a little bit concerned about the result I got in the one I ran with charmm force field. The free energy estimate values looks high. Wanted to be sure there is no over estimation of the interactions between the ZN and the ligand. The ligand is highly charged though. Plsease from experience, do you think these values are normal?

                    ΔG(Kcal/mol)           SD          SEM
IM1-lig1                -592.01      20.73           1.46 

IM78-lig2             -385.26       10.91           0.77

 

The electrostatic component is likely being overestimated. What charge did you use for Zn? According to the per-residue, the two Zn atoms and the ligand have the greater contribution. Probably the charge used is too high. Certainly, these methods have not been parameterized for this type of system. However, you can vary the internal dielectric constant or use a non-linear PB solver to intend to reduce the electrostatic contribution overestimation. In any case, as it is a comparison, you can use relative terms, since it is assumed that the error should be similar in both cases. 

[John]

Thank you Mario. I used the non-linear PB solver and it reduces the electrostatic estimation. 

However, in some trajectories I got this error. How do I solve this please? Thank you.

[INFO   ] Using ligand structure from complex to generate AMBER topology

[INFO   ] Normal Ligand: Saving group 14 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb

  File "/home/alaooj/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/alaooj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/alaooj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 548, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()

  File "/home/alaooj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 116, in buildTopology
    self.gmx2pdb()
  File "/home/alaooj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 436, in gmx2pdb
    self.resi, self.resl, self.orderl = res2map(self.indexes, self.complex_str)
  File "/home/alaooj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 558, in res2map
    for e in value['num']:
TypeError: string indices must be integers
Error occurred on rank 0.

Exiting. All files have been retained.

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

[marioe911116]

This error has been reported previously. please check these threads:

https://groups.google.com/g/gmx_mmpbsa/c/YiwdRf_MRqY/m/rAQK7nkOBAAJ

https://groups.google.com/g/gmx_mmpbsa/c/8aEUDNJzT2E/m/1f2iBHSbDQAJ

and if that works for you

[Alao, John-Paul]

Thank you it worked. The error was due to index mismatch. 

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[marioe911116]

great!