Good to know Jason. I am trying the python script now and currently holding on the following for few minutes already without seeing any changes:
[* binding_MMPBSA.py]$ MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp com.prmtop -cp com_vac.prmtop -rp rec_vac.prmtop -lp lig_vac.prmtop -y galk.clean.mdcrd
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /*/amber14/bin/mmpbsa_py_energy
cpptraj found! Using /*/amber14/bin/cpptraj
Preparing trajectories for simulation...
Any idea?
-Sook Wong
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Thursday, November 06, 2014 3:19 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Binding energy using mm_pbsa.pl
On Thu, Nov 6, 2014 at 3:05 PM, Wong, Sook (NIH/NCATS) [V] < sook.wong.nih.gov> wrote:
> Hi Aron,
>
> The python version is it using the MMPBSA.py method?
>
Yes. That is the version I know the best and the only one I really have the time to help with issues.
There are a number of differences between mm_pbsa.pl and MMPBSA.py -- in particular the input files for MMPBSA.py are the same Fortran namelist-style input that sander and pmemd accept.
You are likely to find that MMPBSA.py receives more support from the mailing list than the Perl version.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Nov 06 2014 - 12:30:04 PST
