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

From: David A Case <>
Date: Wed, 31 May 2017 08:15:22 -0400

On Wed, May 31, 2017, Nikolay N. Kuzmich wrote:
> 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.
> Here I enclose the copies of both my and test files.
> Except for the atom enumeration, couldn't find major differences...

There may be something wrong with your xleap: I can't reproduce the problem.
I did this:

SUS = loadmol2 sustiva_nick.mol2
edit SUS

I don't see any dummy atoms. Any you can see via a text editor that there
are no dummy atoms in your mol2 file.

Right now, I don't have any more suggestions. In xleap, you could turn
on the atom labels, and see what xleap says the name of the dummy atom is:
maybe that will offer a clue. But if this is the only problem, you can
probably ignore it, and continue with your work.


AMBER mailing list
Received on Wed May 31 2017 - 05:30:04 PDT
Custom Search