AMBER Archive (2004)

Subject: Re: AMBER: antechamber prepin

From: David A. Case (case_at_scripps.edu)
Date: Mon Mar 08 2004 - 00:49:48 CST

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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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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