[gmx-users] HA atom not recognised by gromacs

jayalakshmi sridhar jayasri1969 at gmail.com
Fri Sep 11 17:39:43 CEST 2009

Dear Gromacs users,
I have a homology model of a protein. Te N-terminal is an ASP residue. When
I run the command
pdb2gmx -f protein.pdb -o protein.gro -ff G43a1 -p protein.top -i posre.itp
I get the following error-
Atom HA in residue ASP 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.
The protein looks alright in Sybyl. How to get this working? Thanks for the
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