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 - 10:30:02 PDT
