[gmx-developers] query regarding protein-ligand simulation

John Whittaker johnwhittake at zedat.fu-berlin.de
Wed Jun 10 20:26:00 CEST 2020


This question is better-suited for the GROMACS user forum:


This mailing list is for developers and those working on the code itself.
Repost your question there with more detail about the command you issued
and someone should be able to help.

I believe (though I haven't simulated proteins or used pdb2gmx in a while)
that the error is due to a mismatching of atom names in the pdb you are
supplying and the rtp file that GROMACS uses to construct the
topology/coordinate file/etc (i.e., your pdb has the atom HN1 present in
the residue PHE, but the rtp entry for PHE does not have an atom called
HN1, so GROMACS doesn't know what to do). At least I think that's the



> 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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