[gmx-users] mutating the protein

[Repic Matej]

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
--nogui

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

Best,


------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ­ LCBC
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:

>Hi!
>
>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
>I
>wanted to mutate the protein by replacing one particular amino acid by
>another one. How may I do that?
>
>Thank you in advance!
>
>-- 
>Regards,
>Raag
>-- 
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