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
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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--
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/
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Received on Mon Jun 29 2015 - 05:00:02 PDT
