Hi Norbert,
I have discussed this issue several times now and most recently in the
thread "MMGBSA on Protein-DNA/RNA complex" ... Please spend some time to
read those messages carefully (the entire AMBER forum is archived and
can be easily searched). Its quite unproductive to repeat same answers
to different threads. If you have further and more specific questions
that were not addressed in previous threads, I am happy to help further.
Best wishes
Vlad
On 06/29/2015 01:31 PM, Norbert GARNIER wrote:
> Thank you for your reply,
>
> As you advice me, I performed MMPBSA caculation using AmberTools15.
> However I obtained positive binding energy values!
> Could you please advice me?
>
> Thank you very much.
> Norbert
>
> Le 24/06/2015 19:06, Ray Luo, Ph.D. a écrit :
>> Norbert,
>>
>> It's always better to use the latest release to get good support. Note
>> AmberTools is free and is just updated for this year …
>>
>> All the best,
>> Ray
>>
>> --
>> Ray Luo, Ph.D.
>> Professor,
>> Biochemistry, Molecular Biophysics, Chemical Physics,
>> Chemical and Biomedical Engineering
>> University of California, Irvine, CA 92697-3900
>>
>> On Wed, Jun 24, 2015 at 8:32 AM, Norbert GARNIER <
>> norbert.garnier.cnrs-orleans.fr> wrote:
>>
>>> Dear Jason,
>>>
>>> I am using amber11 and a 2.4.3 python version.
>>>
>>> Norbert
>>>
>>> Le 23/06/2015 14:37, Jason Swails a écrit :
>>>> On Tue, Jun 23, 2015 at 8:26 AM, Norbert GARNIER <
>>>> norbert.garnier.cnrs-orleans.fr> wrote:
>>>>
>>>>> Dear Amber Users
>>>>>
>>>>> I have performed 10 ns of MD simulations on a DNA-Protein-Ligand-Na+ and
>>>>> a zinc atom complex with Amber11.
>>>>> I would like to calculate the binding free energy of the ligand with the
>>>>> DNA-Protein part using MMPBSA.py.
>>>>>
>>>>> My input file is the following:
>>>>>
>>>>> &general
>>>>> startframe=1, interval=5, endframe=5000, keep_files=2
>>>>> receptor_mask=':1-299', ligand_mask=':300',
>>>>> strip_mdcrd=1, strip_mask=':Na+:ZNA',
>>>>> entropy=1,
>>>>> /
>>>>> &pb
>>>>> nopot=1, cavity_surften=0.0378, cavity_offset=-0.5692,
>>>>> fillratio=4, scale=2.0,
>>>>> linit=1000, prbrad=1.4, radiopt=0,
>>>>> /
>>>>>
>>>>>
>>>> Is this input file is correct?
>>>> What is nopot? That doesn't look like any MMPBSA.py variable I'm aware
>>>> of... And your strip_mask only strips Na+ and ZNA residues. Did you not
>>>> have explicit solvent?
>>>>
>>>> Also, what version of AmberTools are you using?
>>>>
>>> --
>>> Dr. Norbert GARNIER
>>> Assistant Professor of physics - Orléans University
>>>
>>> « DNA repair: structural and functional approaches»
>>> Centre de Biophysique Moléculaire, UPR4301, CNRS
>>> Rue Charles Sadron
>>> CS 80054
>>> 45071 Orléans cedex 2
>>> Tel: +33 (0)2 38 25 76 68
>>> Web site : http://cbm.cnrs-orleans.fr/
>>>
>>> _______________________________________________
>>> 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
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
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/43241/cojocaru
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Received on Mon Jun 29 2015 - 05:00:03 PDT
