Re: problem in running MM-PBSA script

From: David Case <>
Date: Thu 14 Feb 2002 08:42:52 -0800

On Thu, Feb 14, 2002, thenmalar rathinavelan wrote:

> I am trying to calculate binding free energy a DNA
> system using MM-PBSA. For that, I have used the script
> given in /src/mm-pbsa/EXAMPLE1 directory ...

> But, all the three try*all.out files contain only the
> energy components of one (first) structure (I am
> trying to do the calculations for a crd file which has
> 100 structures) and in try_GB_new_statistics.out all
> the "std" are given as "nan".

If you have only one structure, there is no relevant standard deviation,
but the program does not gracefully check for that problem.

What did you use for your TRAJECTORY? Are you sure (e.g. from running
ptraj) that it has the appropriate number of snapshots?

> Also, I am unable to get "md5_crd1.Z" file from the
> AMBER web page. I like to know whether it is possible
> to get that co-ordinates also.

You can get this via anonymous ftp from, in the directory

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Thu Feb 14 2002 - 08:42:52 PST
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