[gmx-users] gromacs error

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 30 18:58:41 CET 2009

pawan raghav wrote:
> I am using Gromacs on windows hen executing pdb2gmx command, I got an 
> error i.e.
> Fatal error: Atom HD1 in residue HISB 3 not found in rtp entry with 14 
> atoms while sorting atoms. May be different protonation state. Remove 
> this hydrogen or choose a different protonation state.
> I want to know what is the error type and where is rtp entry.

Please read the manual.  Also, consult the following:


If you want more descriptive advice, provide us with your actual command line, 
snapshots of the .pdb file, etc.


> -- 
> Pawan


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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