A change in every single parameter in PBSA can change your dG value quite drastically as well as its sign. We saw quite large differences between sasopt=0 and sasopt=2 and between different values of the internal dielectric constant (see Merino et al Structure 2014). For systems like your I would really advise you to play with the PBSA input directly and use the MMPBSA.py just as an interface for running the jobs with your predefined inputs.
Vlad
On June 23, 2015 2:26:07 PM CEST, 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?
>
>With this input file I obtain positive DELTA G binding value.
>
>Could you please give me some advices?
>Thank you very much.
>
>Norbert
>
>--
>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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--
Sent from my Android device with K-9 Mail. Please excuse my brevity.
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Received on Tue Jun 23 2015 - 06:00:03 PDT
