On Fri, Jun 10, 2011 at 7:51 AM, Guenegou, Guillaume [ORDFR] <
GGUENEGO.its.jnj.com> wrote:
> Dear all,
>
> I work with amber11 and AmberTools1.5.
>
> I want to use alanine scanning protocol with mm_pbsa.pl and I get the
> following error message:
>
> "Prmtop ../../leap/FABI_C01_ChainD_2_wat/FABI_C01_ChainD_2.top and
> coord.file ./1_2_com.crd.1 have different atom numbers
> For details see:
> http://ambermd.org/Questions/mm_pbsa.html#check_atom_nr_prmtop_and_crd_d
> iffer
> at /clu01/applic/amber11/src/mm_pbsa/mm_pbsa_calceneent.pm 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?
>
Yes.
> In that case, I don't understand the interest of alanine scanning
> protocol with mm_pbsa.pl
>
> If someone has an idea...
>
It allows you to calculate the binding free energy of a particular alanine
mutant *without* running a new simulation. (Subject to certain limiting
assumptions, of course).
HTH,
Jason
> Regards,
> G.GUENEGOU
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 10 2011 - 07:30:03 PDT
