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 ?
The second possibility if one would like to "play" more with all entropy
associated
parameters he may use directly NAB (not NAB called from MMPBSA.py) to
calculate entropy
of his system. Am I right ?
Best wishes,
Marek
Dne Thu, 13 Mar 2014 02:24:35 +0100 Jason Swails <jason.swails.gmail.com>
napsal/-a:
> On Wed, Mar 12, 2014 at 8:40 PM, Marek Maly <marek.maly.ujep.cz> wrote:
>
>> Dear all,
>>
>> I had recently some problems with receptor entropy
>> calculations (minimization phase) using MMPBSA.py.MPI
>> so I wanted to check/edit relevant parameters so I
>> used -make-mdins in the command hoping to obtain
>> input files:
>>
>> _MMPBSA_sander_nm_min.mdin
>> _MMPBSA_nmode.in
>>
>> But MMPBSA.py.MPI as well as MMPBSA.py program
>> just wrote these two lines and exited.
>>
>> ----------------------------------------------------
>> Loading and checking parameter files for compatibility...
>> Created mdin files. Quitting.
>> ---------------------------------------------------
>>
>> No mdin files was created in spite the information written by
>> the program.
>>
>> Interestingly, this problem appears just in case of entropy calculation.
>> If I switch to PB,GB or APBS calculation, the -make-mdins flag works
>> perfectly and relevant mdin files (_MMPBSA_gb.mdin,_MMPBSA_pb.mdin ...)
>> are successfully
>> created.
>>
>> I am using patched actual version of Ambertools13 and Amber12 and I
>> tested
>> this issue on two
>> different machines and also on two different molecular systems.
>>
>
> MMPBSA.py does not use input files for normal mode entropy calculations.
> All available options are exposed in the &nmode section of the input
> file.
> The input files you referred to above were written for minimizing
> snapshots in sander and running normal mode calculations with the nmode
> program.
>
> Normal mode calculations are now run with a nab program that is invoked
> through command-line flags.
>
> HTH,
> Jason
>
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 13 2014 - 07:30:02 PDT
