The easiest way I know of is using Swiss-Pdb (you can download it for free from
http://us.expasy.org/spdbv/). Its as easy as selecting the residue of interest and changing it and saving the pdb file.
siva
-----Original Message-----
From: Ioana Cozmuta [mailto:ioana.nas.nasa.gov]
Sent: Monday, October 27, 2003 6:46 PM
To: Amber List
Subject: AMBER: aminoacid mutation
Hi amber 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 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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Received on Tue Oct 28 2003 - 15:53:00 PST
