Hi Jason,
Thanks for the response.
It so happens, that something was wrong with my complex.topology file that
was causing the failure with the MMPBSA calculations. It is now fixed and I
am able to run MMPBSA.py.
However, I noticed another message when I run my calculations.
python/2.7.6-gcc-
4.8.2_140404/lib/python2.7/sitepackages/numpy/oldnumeric/__init__.py:11:
ModuleDeprecationWarning: The oldnumeric module will be dropped in Numpy
1.9
warnings.warn(_msg, ModuleDeprecationWarning)
The job seems to be finish fine in spite of this error. I am currently
running the serial version i.e. MMPBSA.py.
I was just wondering what might cause this and If I should be worried about
this?
Thanks.
On Tue, Nov 24, 2015 at 10:24 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Tue, Nov 24, 2015 at 11:46 AM, Vivek Bharadwaj <
> vbharadw.mymail.mines.edu
> > wrote:
>
> > Dear Amber users,
> >
> > I am trying to perform binding energy decomposition energies for a
> > substrate bound protein system that has a Heme bound. I am using Amber14
> > with Ambertools15.
> >
> > I understand that Sander requires the radius for Fe atom which requires
> > modification of the mdread2.F90 file and recompiling of sander.
> >
> > I followed the instructions based on this previous query (
> > http://archive.ambermd.org/201412/0132.html) and modified the
> mdread2.F90
> > file and also recompiled sander. I also re-generated the complex, ligand
> > and receptor topologies after recompiling amber.
> >
>
> Regenerating the topology files is unnecessary.
>
>
> > However, I still get the following error while performing decomp
> > calculations. I am able to run normal mmgb/pbsa calculations without
> decomp
> >
> > though.
> >
>
> Are you sure you modified the correct part of mdread2.F90? There are two
> locations where these radii need to be set. The first is when gbsa=1
> (which I believe occurs first in the source code file) and the second is
> where gbsa=2. Decomposition uses gbsa=2. So I suspect you needed
>
> to make this change in a second place in order for it to work for your
> application.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Vivek S. Bharadwaj
Postdoctoral Researcher
National Renewable Energy Laboratory
Golden Colorado
http://inside.mines.edu/~vbharadw/
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Received on Wed Nov 25 2015 - 09:30:02 PST
