VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Oct 28 2003 - 10:22:38 CST

Hi Ioana

Doesn't psfgen have a mutate command that will do what you described
below.
After reading in all the segments you can use mutate resid resname to
change the residue if I am not mistaken.

Brian

On Mon, 27 Oct 2003, Ioana Cozmuta wrote:

> Hi vmd users,
>
> Is there a way to "automatically" mutate an aminoacid from a protein
> structure into another one. Say I want to replace an ALA aminoacid with a
> LEU aminoacid. Is it possible just to select the ALA aminoacid I want to
> mutate and turn it into LEU? Is there some other software out there that
> could do this on a more automatic basis?
> The way I thought doing it was to edit the pdb file myself and try to edit
> the coordinates of the atoms in the new aminoacid such that the bond
> lengths are preserved and then equilibrate the new positions. But then my
> boss told me to try "not to lose time with this" and find a software that
> does it automatically :)
>
> Any suggestions are welcomed!
> Thanks,
> Ioana
> 

-- 
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**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448    bennion1_at_llnl.gov                     **
**7000 East Avenue       phone: (925) 422-5722                 **
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