On Fri, 2014-04-25 at 18:17 +0400, James Starlight wrote:
> Jason,
>
> many thanks!
>
>
>
> the addition of the
>
> &general
> endframe=150, keep_files=2, strip_mask=':WAT,CLA,POT,POPE,POPC'
>
>
> have been solved problem.
>
>
> In the manual I've found that using gb=2
> " PBradii mbondi2" to prepare the prmtop file should be set.
>
> Does some modification of the --radii=RADIUS_SET variable or some
> other radius definitions are needed for such calculations?
Yes, when running ante-MMPBSA.py you should use "--radii=mbondi2" to
generate the mbondi2 radii for your system.
Alternatively, you can use the "changeRadii mbondi2" command in ParmEd
to do this to the topology files you already have. (ante-MMPBSA.py
actually uses ParmEd behind-the-scenes).
>
>
> What else options for the mm-pbsa should be taken into account in case
> of the dG of ligand- membrane proteins estimations?
You should go through the options in the manual, and maybe
cross-reference the options there with what you have seen people use in
other (related) studies.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Apr 25 2014 - 08:30:03 PDT
