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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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