Re: [AMBER] mmpbsa_py_energy and PBSA options

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Fri, 25 Oct 2013 11:54:27 -0700

I see, sorry for the confusion. Then cutnb = 12 should be certainly
fine. It's for the van der Waals energies. Electrostatics is still
computed without cutoff.

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 11:18 AM, Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Yes, but cutnb=0 is not acceptable for eneopt=1 ....
>
> Vlad
>
>
> On 10/25/2013 07:52 PM, Ray Luo, Ph.D. wrote:
>> 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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>>
>>> --
>>> 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
>>>
>>>
>>> _______________________________________________
>>> 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
>>
>>
>
> --
> 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
>
>
> _______________________________________________
> 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 - 12:00:03 PDT
Custom Search