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

From: Nikolay N. Kuzmich <>
Date: Wed, 31 May 2017 14:43:20 +0300

Dear David and Amber users,

I use Amber 14/AmberTools 15 version.
The OS is OpenSuse 13.2.
The complilers in use are gcc (SUSE Linux) 4.8.3 20140627 and
GNU Fortran (SUSE Linux) 4.8.3 20140627.
Executing the "Run.sustiva" script gave optimistic results:

antechamber/sustiva# ./Run.sustiva
diffing with sustiva.mol2
diffing with frcmod
diffing with leap.out
diffing with prmtop

Here I enclose the copies of both my and test files.
Except for the atom enumeration, couldn't find major differences...

Thank you in advance,

Message: 8
Date: Mon, 29 May 2017 12:17:56 -0400
From: David Case <>
Subject: Re: [AMBER] Dummy atoms when running antechamber in B4
        (sustiva) tutorial
To: AMBER Mailing List <>
Message-ID: <>
Content-Type: text/plain; charset=us-ascii

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 Wed May 31 2017 - 05:00:02 PDT
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