[gmx-users] mutating the protein

[Catarina A. Carvalheda dos Santos]

Hi there,

I don't know about other options, but PyMOL allows you to do this using the
"Mutagenesis Wizard" (just google it and you'll find step-by-step
instructions in the PyMOL Wiki).
Whatever you use, make sure that you select a proper side chain orientation
(rotamer) when performing the mutation. This will avoid clashes between
protein atoms and therefore problems during the energy minimization step.

Regards,




On 30 September 2015 at 12:19, Repic Matej <matej.repic at epfl.ch> wrote:

> 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
> >--
> >Gromacs Users mailing list
> >
> >* Please search the archive at
> >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >posting!
> >
> >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >* For (un)subscribe requests visit
> >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >send a mail to gmx-users-request at gromacs.org.
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
School of Life Sciences
University of Dundee
DD1 5EH, Dundee, Scotland, UK