Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial

From: David Case <>
Date: Mon, 29 May 2017 12:17:56 -0400

On Mon, May 29, 2017, Nikolay N. Kuzmich wrote:
> In Sustiva/B4 tutorial I ran antechamber to convert sustiva_new.pdb file
> into sustiva.mol2 file and to compute the bcc charges.
> When the mol2 file was loaded into xleap and checked, unexpectedly the
> dummy atoms in structure were seen.

Something is definitely wrong: there should be no dummy atoms in the mol2
file. I can't reproduce your problem--just ran the tutorial myself, and
everything looks fine.

So: what version of AmberTools do you have? What compiler and OS?

In the $AMBERHOME/AmberTools/test/antechamber/sustiva directory, there is
a "Run.sustiva" script which is part of the test suite. Does this PASS
for your system? If not, you have a bad installation. If it PASSES, try
to find the difference between what you did and what is in this test

...good luck....dac

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Received on Mon May 29 2017 - 09:30:03 PDT
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