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

annalisa bordogna annalisa.bordogna at gmail.com
Mon Feb 8 09:36:42 CET 2010


Since you have modelled the structure, so the important thing is the
position of the heavy atoms and not of the hydrogens, you can just do what
GROMACS asks you to do:

pdb2gmx ..... (all the things that you have to put) ...... -ignh

This flag will make pdb2gmx ignore the hydrogens and replace them.

Hope it helps!


Annalisa Bordogna - PhD. student
Universita` degli Studi di Milano - Bicocca - Italy

2010/2/8, bharat gupta <bharat.85.monu at gmail.com>:
> 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
> --
> Bharat
> M.Sc. Bioinformatics (Final year)
> Centre for Bioinformatics
> Pondicherry University
> Puducherry
> India
> Mob. +919962670525
> --
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