On Fri, Mar 20, 2015 at 11:32 AM, Norbert GARNIER <
norbert.garnier.cnrs-orleans.fr> wrote:
> Dear amber list,
>
> I am using MMPBSA.py (amber11) to compute the binding free energy of a
> (Protein-dna)-ligand complex
> with /usr/local/amber11/src/mmpbsa_py/MMPBSA.PY
> My input file is the following:
>
> &general
> startframe=1, interval=50, endframe=5000, keep_files=2,
> receptor_mask=':1-299', ligand_mask=':300',
>
I would suggest letting MMPBSA.py figure out the receptor_mask and
ligand_mask on its own (i.e., by removing these variables from the input
file). Easier to avoid mistakes that way.
> strip_mdcrd=1, strip_mask=':Na+:ZNA',
> /
> &pb
> istrng=0.000, exdi=80.0, indi=1.0,
> inp=2, cavity_surften=0.0378, cavity_offset=-0.5692,
> fillratio=4, scale=2.0,
> linit=1000, prbrad=1.4, radiopt=1,
> /
>
> I have the following message:
> Warning: Input error! "inp=2" is an invalid option.
>
As Kenneth said, upgrade to AmberTools 14 to use MMPBSA.py. The inp=2
model was introduced after Amber 11.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 20 2015 - 09:30:04 PDT
