[gmx-users] mutating the protein

Repic Matej matej.repic at epfl.ch
Wed Sep 30 13:19:25 CEST 2015

I do not think this is something gromacs supports, but you can use several
other programs like VMD, Chimera, Modeler etc, depending on the method of
mutating a residue. I usually use chimera on macosx or linux like this:

echo "open protein.pdb; swapaa leu :333.a; write 0 333leu.pdb" | chimera

This command opens the protein.pdb, swaps the amino acid 333 on chain a,
and saves the pdb as 333leu.pdb.


Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
BCH 4108
CH - 1015 Lausanne

On 9/30/15, 11:55, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Raag Saluja" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se
on behalf of saluja.raag at gmail.com> wrote:

>Gromacs is a beautiful software!  I have been able to understand the
>dynamics of this protein I was trying to study.
>I wanted to see how the various amino acids could affect its dynamics. So
>wanted to mutate the protein by replacing one particular amino acid by
>another one. How may I do that?
>Thank you in advance!
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