On Thu, Mar 13, 2014 at 9:58 AM, Marek Maly <marek.maly.ujep.cz> wrote:
> Thanks Jason,
>
> so at this moment if one would like to change some advanced/additional
> settings in case of entropy calculation using MMPBSA.py he may
> do it perhaps just via those command-line flags (they are perhaps
> described in NAB documentation ? ) which are used for the command based
> invoking of the NAB program,
> from MMPBSA.py script am I right ?
>
You can try to deduce what the command-line flags are for
mmpbsa_py_nabnmode (the program that actually gets run by MMPBSA.py to
compute normal modes), but I don't think you'll get any added flexibility
using the program directly compared to specifying variables in the
MMPBSA.py input file.
If you really want to customize the normal mode calculation you'll need to
write your own nab program that performs it the way you want it performed.
The back of the AmberTools manual describes the syntax of the NAB
programming language (and you can use mmpbsa_entropy.nab in
$AMBERHOME/AmberTools/src/mmpbsa_py to get started).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Mar 13 2014 - 11:00:03 PDT
