VMD-L Mailing List

From: Justin Gullingsrud (jgulling_at_mccammon.ucsd.edu)
Date: Tue Oct 28 2003 - 10:55:42 CST

On Oct 28, 2003, at 8:22 AM, Brian Bennion wrote:

> 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.
>

Not exactly; the mutate command is used within the segment statement
and basically just renames the residue. It doesn't change existing
segments. If you wanted to do that, you would have to write out a pdb
of the whole chain, then read it back into psfgen from within a segment
statement that had the mutate command.

Justin

> 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
>>
>
> --
> *****************************************************************
> **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 **
> **Livermore, CA 94550 fax: (925) 422-6605 **
> *****************************************************************
>
> 

--
It is easier to make a theory of everything, than a theory of 
something. -- Aharon Katchalsky