Re: [AMBER] mmpbsa_py_energy and PBSA options

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Fri, 25 Oct 2013 09:56:01 -0700

Vlad,

The python and perl scripts only accept a very limited set of options
for PBSA. To test with all the options, you have to use PBSA program
directly. Its user interface is like the SANDER program.

All the best,
Ray 
--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Fri, Oct 25, 2013 at 9:02 AM, Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Dear all,
>
> When using mmpbsa_py_energy in MMPBSA.py and trying to change PBSA
> options in _MMPBSA_pb.mdin, I get lots of weird errors.
> Several options listed as PBSA options in the manual (e.g. ipb, sasopt,
> triopt) are not accepted. Also when I specifically set eneopt = 2 in the
> _MMPBSA_pb.mdin file, the calculation exists with an error saying that
> eneopt = 1 requires a non-zero cutnb as if the input is not read correctly.
>
> I guess given all these problems with mmpbsa_py_energy, it is
> recommended to use sander (by setting use_sander=1)
>
> Best
> Vlad
>
> --
> Dr. Vlad Cojocaru
> Max Planck Institute for Molecular Biomedicine
> Department of Cell and Developmental Biology
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 25 2013 - 10:00:03 PDT
Custom Search