AMBER Archive (2005)

Subject: Re: AMBER: Antechamber -reorders atom sequence

From: David A. Case (case_at_scripps.edu)
Date: Thu Apr 14 2005 - 09:53:17 CDT

On Thu, Apr 14, 2005, Austin B. Yongye wrote:

> I am using Antechamber to generate a prep file from a gaussian output file.
> Problem is that Antechamber writes a prep file with atom sequences that
> are different from those in the gaussian output file.

The format of the prep file requires that the atoms be ordered according to
a covalent bond tree. So what you see is expected.

If you want to create units with a given ordering, use the mol2 format,
instead of prepi. In general, the "prepi" format is not really needed for
anything (we tend to use mol2 instead). You then use "loadMol2" rather than
"loadAmberPrep" to get the unit into LEaP.

The prepi format is really obsolete, and will be deprecated in future releases
of antechamber, (kept only for backwards compatibility with a program that was
first written in the late 1970's).

...hope this helps...dac

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