[gmx-users] Keeping portions of a protein fixed during energy minimization and MD simulations

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 28 01:53:00 CEST 2008

shyamala iyer wrote:
> Hi all,
> I have a question regarding keeping certain protein residues fixed
> during EM and MD simulations. I wish to keep a portion of the protein
> fixed while minimizing the residues close to the ligand and ligand
> binding site. Is there a way to accomplish this?

Create an index group with make_ndx that contains the portion of the protein you 
want to keep fixed.  Then pass this index file to genpr with the -n flag.


> Thanks,
> Shyamala Iyer
> Department of Microbiology,
> U Washington, Seattle
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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