Re: [AMBER] Problem when calculating MMPBSA

From: Jason Swails <>
Date: Fri, 27 Dec 2013 02:03:35 -0500

On Fri, Dec 27, 2013 at 1:50 AM, dongying0512 <> wrote:

> Hi all,
> I have a problem when calculating MMPBSA, and i'm not sure where this
> error is coming from. Please help me out. Thamks in advance.
> And all of the nput files and results are attached.
> dy.ubuntu:~/Work$ $AMBERHOME/bin/ -O -i -o RESULT.dat
> -sp DNA_AMP_wb_vmd.prmtop -cp DNA_AMP_ante.prmtop -rp DNA_ante.prmtop -lp
> AMP_ante.prmtop -y test.dcd
> Loading and checking parameter files for compatibility...
> sander found! Using /home/dy/amber12/bin/sander
> cpptraj found! Using /home/dy/amber12/bin/cpptraj
> Preparing trajectories for simulation...
> 10 frames were processed by cpptraj for use in calculation.
> Running calculations on normal system...
> Beginning PB calculations with /home/dy/amber12/bin/sander
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
> ValueError: could not convert string to float: EEL
> Exiting. All files have been retained.

This is very strange. Please make sure you have applied all updates (and
recompiled AmberTools 13). If you are still getting this error, can you
create a tarball of the necessary topology files and a trajectory file with
2 snapshots so I can try to reproduce this error? You can send me the
files off-list.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Dec 26 2013 - 23:30:02 PST
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