AMBER Archive (2006)

Subject: Re: AMBER: charge redistribution in .prep files

From: David A. Case (
Date: Mon Feb 20 2006 - 10:29:41 CST

On Mon, Feb 20, 2006, Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) wrote:

> We noticed that the order of the atoms in this new .prep file was altered
> with respect to the order in the preciding .prep file and the pdb file ....

This is a known limitation. You can use the mol2 format (instead of prepi)
to get around this problem. We generally recommend that users use the mol2
format in place of prepi for these sorts of calculations.

[Note: if you use the search bar at the Amber web site, and search on "atom
order antechamber" in the mailing list archives, you will find this problem
and solution discussed many times.]

...good luck...dac

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