[gmx-developers] query regarding protein-ligand simulation

Sanah Singh snazzy.simon at gmail.com
Wed Jun 10 19:47:29 CEST 2020

Dear Sir/maam

I want to perform an MD simulation of a  protein-ligand complex. I followed
the Justin A. Lemkul tutorial for the protein-ligand complex. The tutorial
went smoothly. Next, I tried with my complex that is, I have docked a
ligand with the protein of interest using autodock 1.5.6

Upon running the pdb2gmx command, it shows an error. : Fatal error:
Atom HN1 in residue PHE 3 was not found in rtp entry PHE with 22 atoms
while sorting atoms.

I understand that the gromacs is not able to recognize the file due to atom
numbering. But how to solve this issue, as I don't know what forcefield
will be compatible with this file.

Kindly help me in this regard.
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