[gmx-users] genion command with PDB files for amber03 force field

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 5 15:49:43 CET 2009

drugdesign wrote:
> Dear gromacs users,
>  I am using genion command to add ions to .tpr file which
> was made for protein by use of amber03 force field. 
> In intial pdb file N-terminal amino acid is NHIE, but genion changes it to NHI, which isnot recognized by next pdb2gmx.

PDB format dictates 3 characters for writing residue names.  If you want to keep 
NHIE, use .gro format.  What "next pdb2gmx" are you talking about?  If you've 
written your topology (the first step), there should be no reason to run pdb2gmx 
again during system preparation.


> This is not a big problem , but it looks is a little bit like a bug.
> Best regards,
> Andrew
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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