[gmx-users] provide opt way to perform simulation for protein and peptide -reg

Justin Lemkul jalemkul at vt.edu
Fri Sep 28 16:32:46 CEST 2012

On 9/28/12 10:07 AM, venkatesh s wrote:
> Respected gromacs Users,
>                                           i want perform stimulation for
> protein + peptide (in water medium only not membrane protein)
> 1. Can i use the Docked conformation (better conformation both protein +
> peptide make it as one file .pdb ) for perform simulation


> 2. Other than that manually edit the coordinate file  after TER or END
> insert peptide amino acid (my peptide having a 5 amino acid )

I don't understand what you want to do here.  pdb2gmx can deal with multiple 
proteins in a single coordinate file, with topologies written for each depending 
on what you choose for the -chainsep option.  Different chain identifiers or TER 
delimiters can be used to indicate that a new molecule has started.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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