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

[bharat gupta]

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