Re: [AMBER] Query regarding energy calcuation using 3D-RISM

From: David Case <>
Date: Sat, 20 May 2017 22:23:57 -0600

On Sun, May 21, 2017, Vertika Gautam wrote:
> I tried running non-parallel on similar system. This time getting new error
> line 1204, in check_length
> (key, len(self.parm_data[key]), length))
> AmberParmError: FLAG ATOMIC_NUMBER has 73052 elements; expected 7940
> Exiting. All files have been retained.

Please (re-)read the second paragraph of Chap. 30, (p.686) of the Reference
Manual. Basically, the mmpbsa scripts automate a large number of steps,
and can be quite helpful in the case where everything works. But there
are many, many ways in which things can go wrong, and the scripts are only
partially successful in capturing errors. So you need to be sure to
run a short simulation "by hand", creating yourself the three required prmtop
files, and the corresponding trajectory files, and examine how the scripts
extract the appropriate energies from the resulting MD output files.

Second, be sure to examine all the output files carefully. Often problems
are evident in these. As a guess, but sure to specify exactly what the
receptor and ligand residues are, instead of relying upon the scripts to
figure this out for you (the scripts sometimes get this wrong.)

Third, the error message above should be helpful in debugging. Which value
for the number atoms is correct (73052 or 7940)? Can you look at the prmtop
files you have and see what the ATOMIC_NUMBER section has, looking for
anything odd.

....good luck....dac

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Received on Sat May 20 2017 - 21:30:02 PDT
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