Re: [AMBER] Alanine scanning

From: Bill Miller III <>
Date: Fri, 10 Jun 2011 10:01:53 -0400

In order to run alanine scanning, you will need to create topology files
with the mutant residues because otherwise sander cannot be run to calculate
the energies if no corresponding topology files exists with the coordinate
file. The perk to alanine scanning is one can get an idea of how much a
mutation to alanine at a certain spot in the protein affects the binding
affinity without to explicitly run a new MD simulation with the mutant
residue. Alanine scanning is much more time efficient than running a new

Of course, one could also use decomposition analysis as an alternative to
alanine scanning, depending on what you want to get out of the calculation.
And decomposition analysis does not require additional topology files,

I hope that helps.


On Fri, Jun 10, 2011 at 9:51 AM, Guenegou, Guillaume [ORDFR] <> wrote:

> Dear all,
> I work with amber11 and AmberTools1.5.
> I want to use alanine scanning protocol with and I get the
> following error message:
> "Prmtop ../../leap/FABI_C01_ChainD_2_wat/ and
> coord.file ./1_2_com.crd.1 have different atom numbers
> For details see:
> iffer
> at /clu01/applic/amber11/src/mm_pbsa/ line 1137."
> I guess this different atom number comes from the fact that the
> coord.file contains mutant residues, so the number of atoms is different
> from the one in topology file.
> Does it mean I have to generate a topology file with mutant residues
> before launching alanine scanning?
> In that case, I don't understand the interest of alanine scanning
> protocol with
> If someone has an idea...
> Regards,
> _______________________________________________
> AMBER mailing list

Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Jun 10 2011 - 07:30:03 PDT
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