Re: [AMBER] energy decompistion stopped

From: Jason Swails <>
Date: Mon, 21 Mar 2011 18:24:01 -0700


On Mon, Mar 21, 2011 at 4:41 PM, Eliac Brown <> wrote:

> In case of DCTYPE = 1, the calculation finished without any problem. But
> defining DCTYPE = 3, the calculation stopped without complaining.

How do you know it failed?

> Here is the end of the log file of with DCTYPE=3
> =>> Doing statistics
> =>> Reading input
> =>> Reordering files
> Final order:
> 1. snapshot_com.all.out: 1 - 226
> 2. snapshot_rec.all.out: 1 - 225
> 3. snapshot_lig.all.out: 226 - 226
> =>> Reading files
> Reading snapshot_com.all.out
> One more question, in the statistics.out file, I couldn't find the final
> results and it is not printed in any ther files, so I sum all the numbers
> under TGBTOT (in Delta section), is there any easy way?
> Any suggestion would be appreciated.

As far as I know, the perl version of the script does not print out the
final binding free energy numbers; just the decomposition. Furthermore,
simply summing TGBTOT will not give you the total energy, I don't think.
The issue that you have is that inter-residue, non-bonded interactions are
included in both residues. You could write a small awk script to pull out
the necessary values from the output files (if you kept them via the
"verbose" keyword in the input file).

If you have Amber11, provides decomposition functionality and
prints out a decomp summary as well as a final binding energy summary as
well. It also simplifies the input procedure (so it figures out recmap,
ligmap, etc.).

Hope this helps,

Thanks in advance
> Eliac
> P.S. All bugfix was applied.
> P.S. I checked most of the pre-posted questions.
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Mar 21 2011 - 18:30:04 PDT
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