AMBER Archive (2004)

Subject: Re: AMBER: antechamber prepin

From: Guanglei Cui (
Date: Mon Mar 08 2004 - 10:22:40 CST

Nice. It works just the way I like it. In xleap editor, it even displays
double bonds with mol2 format. Thanks a lot.


David A. Case wrote:

> On Sun, Mar 07, 2004, Guanglei Cui wrote:
>>When using antechamber to generate prepin file, antechamber will reorder
>>atoms so that hydrogen atoms are immediately after the heavy atoms they
>>attach to. I'd like to know if there's way to switch off this behavior.
> I don't think you can get around this with the prepi format, since the
> tree structure implied requires the re-numbering. But the mol2 format
> may satisfy your needs, and I don't think it renumbers the atoms.
> In general, we are recommeding people use the mol2 format in place of prepi
> (especially in Amber 8), unless they have some particular need for the latter.
> ...hope this helps...dac
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