Thanks Jason,
meanwhile I identified the source of my problem so for the moment
I will do not need experiment directly with NAB.
Best wishes,
Marek
Dne Thu, 13 Mar 2014 18:44:15 +0100 Jason Swails <jason.swails.gmail.com>
napsal/-a:
> 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
>
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Received on Fri Mar 14 2014 - 04:00:02 PDT
