VMD-L Mailing List

From: Y U Sasidhar (sasidhar_at_chem.iitb.ac.in)
Date: Mon Oct 27 2003 - 22:25:00 CST

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
>
>
>
Deep view or swiss pdb viewer
www.expasy.ch/spdbv 

-- 
 Sasidhar
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Dr. Y. U. Sasidhar, Associate Professor, Department of Chemistry
Indian Institute of Technology, Powai, Mumbai 400 076, INDIA
mailto:sasidhar_at_iitb.ac.in
http://www.chem.iitb.ac.in/~sasidhar
Fax   : (+91-22 ) 2572 3480 (IIT Main), (+91-22 ) 2576 7152 (Chemistry)
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 		 and every Tomorrow a vision of hope
 		 Look well, therefore, to THIS DAY"
                            			(Ancient Indian Wisdom)
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