Re: mm_pbsa and ALA scan

From: Lepsa <lepsik_at_marilyn.uochb.cas.cz>
Date: Wed 29 Jan 2003 17:31:41 +0100

Dear Ahammadunny,
ala scan is useful for determining the energetical contribution of
individual residues or contrary
for "turning off" such contributions. So for example, with AS you calculate
the interaction energy
between (multi) ALA mutated receptor and the ligand.

You have to provide the program with mutated topologies. If you do different
sets of mutants then each
mutant its corresponding topology.

Much more accurate and as well CPU time costly is free energy perturbation.
You can get ddG e.g. between wild-type and
mutant.

Hope this helps.

All the best,

     Martin

----------------------------------------------------------------------------
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----
Martin Lepsik, PhD student            Phone:  +420/2/20183-540, Fax:
+420/2/20183-292
Dept. of Theor Chem & Center for Complex molecular Systems and Biomolecules
Institute of Organic Chemistry and Biochemistry (IOCB)
Flemingovo nam 2,
Czech Academy of Sciences,
166 10, Prague 6,
Czech Rep.
> Hi everyone,
>
>           In mm_pbsa I do not understand how the the option, AS=1, works.
This
> is for the input which starts with .ALASCAN. I was under the impression
that a
> residue in a protein can be mutated to ALANINE and then the free energy
> change associated with this mutation can be calculated. But the program
does
> not seem to work that way. When AS=1 and GC=1 are set with other options
> like MM,GB, or MS, snapshots of the coordinates of the mutated protein are
> written into separate files. But then it gives the error message:'mismatch
> in the number of atoms between the coordinate and the topology files.'
This
> may be because of the fact that the topology file is for the wild type(
before
> the mutation) protein. So it requires a topology file for the mutant.
>
>           Is a topolgy file needed for each mutant ?
>
>                            or
>
>           Is there another option to do this kind of calculation ?
>
>
>           Sincerely yours,
>
>
>          A. PATHIASERIL
>
>          Complex Carbohydrate Research Center
>
>          University of Georgia
>
>          Athens, Georgia.
>
>
>
Received on Wed Jan 29 2003 - 08:31:41 PST
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