sorry but it is npopt=1
In the trj files i dont keep water
Thank you
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/
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Received on Tue Jun 23 2015 - 08:30:03 PDT
