Re: [AMBER] mmpbsa_py_energy and PBSA options

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Fri, 25 Oct 2013 10:52:56 -0700

Yes, for nonlinear PB, you have to live with eneopt=1 ... The default
cutnb = 0 means no cutoff is used.

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 10:08 AM, Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Thanks Ray,
>
> Yes ... I figured that out ...
>
> Maybe one last question ... The eneopt error came from using the
> non-linear PB which appears incompatible with eneopt=2.
>
> What are the eneopt and cutnb recommendations for non-linear PB ? Would
> eneopt=1 and cutnb=12 be acceptable or outrageous ?
>
> Thanks again
> Vlad
>
> On 10/25/2013 06:56 PM, Ray Luo, Ph.D. wrote:
>> 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
>>>
>>>
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>
> --
> 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
>
>
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Received on Fri Oct 25 2013 - 11:00:03 PDT
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