I have simulated a protein-ligand complex by using gromacs software and gromos 54A7 force field was deployed for this purpose. Ligand topology (.itp) file was prepared by usimg ATB server. Now I want to calculate protein-ligand binding free energy by gmx_MMPBSA tool.
Command used:
gmx_MMPBSA -O -i mmpbsa.in -cs analysis_npt.pdb -ci protein_ligand.ndx -cp complex.top -cg 1 13 -ct analysis.xtc
But getting an error:
atom.atom_type = params.atom_types[atom.type]
KeyError: 'NL'
Exiting. All files have been retained.
Please help me to solve the problem
Hi,
'NL' atomtype does not exist on on AMBER forcefields (gmx_MMPBSA are optimized for AMBER). You should try g_mmpbsa instead.
Ricardo J Ferreira Thank you for your valuable advice.
I have tried g_mmpbsa but its was showing Segmentation fault (core dumped). In internet I have checked. And not getting any clue by which I can solve this problem. I have tried with several computers with large RAM. So it's clear for me that it's not a memory problem
If you used Gromos, I would bet for a topology mismatch problem with Amber. Try to check if your atom types belong to the atom types recognized by gmx_MMPBSA (NL is NH3 in Gromos, but what happens in Amber?).
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