[gmx-users] HA atom not recognised by gromacs

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 11 17:52:20 CEST 2009

jayalakshmi sridhar wrote:
> 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 help.

G43a1 is a united-atom force field.  Alpha-carbons are not explicitly 
represented.  So if you pass this structure to pdb2gmx, the program assumes you 
have only the necessary atoms present.  If you have unnecessary hydrogens, use 


> Jaya
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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