[gmx-users] WARNING: WARNING: Residue 1 named MET of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.

[Mark Abraham]

Hi,

On Tue, Jun 13, 2017 at 11:10 PM Rana Rehan Khalid <rrkhalid at umich.edu>
wrote:

> dear sir
>
> I remove the hydrogen from my protein before creating the .top file rather
> then use ignore hydrogen command kindly tell me is it right to remove the
> hydrogen before simulation next gromacs steps
>

We can't decide that for you. Either way, pdb2gmx will build hydrogens back
in for you at standard conformations. Sometimes that is easier than dealing
with problematic atom naming or initial conformations.

Mark


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