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?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jun 23 2015 - 06:00:02 PDT
