[gmx-users] Re: topology file generation for a modeled structure

bharat gupta bharat.85.monu at gmail.com
Mon Feb 8 09:21:51 CET 2010

Hi all,

I have modelled a structure and I want to minimize it using GROMACS
but while generating the topology file using pdb2gmx command I am
getting the following error :-

Atom HN1 in residue LEU 1 not found in rtp entry with 9 atoms
             while sorting atoms. Maybe different protonation state.
             Remove this hydrogen or choose a different protonation state.
             Option -ignh will ignore all hydrogens in the input.

Can anyone help me out to rectify this error

M.Sc. Bioinformatics (Final year)
Centre for Bioinformatics
Pondicherry University
Mob. +919962670525

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