Re: [AMBER] Binding energy using

From: Wong, Sook (NIH/NCATS) [V] <"Wong,>
Date: Thu, 6 Nov 2014 20:24:03 +0000

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:

[*]$ -O -i -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 []
Sent: Thursday, November 06, 2014 3:19 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Binding energy using

On Thu, Nov 6, 2014 at 3:05 PM, Wong, Sook (NIH/NCATS) [V] <> wrote:

> Hi Aron,
> The python version is it using the 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 and -- in particular the input files for are the same Fortran namelist-style input that sander and pmemd accept.

You are likely to find that receives more support from the mailing list than the Perl version.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Nov 06 2014 - 12:30:04 PST
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