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
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 12 2014 - 18:30:02 PDT
