AMBER Archive (2003)Subject: Re: Re[2]: AMBER: antechamber problem
From: David A. Case (case_at_scripps.edu)
Date: Thu Aug 21 2003 - 18:34:17 CDT
On Thu, Aug 21, 2003, Junmei Wang wrote:
>
> This molecule has a Zinc atom and amber7 cannot handle it properly. Please
> try the latest version of antechamber in amber8, it should works given the
> atom connectivity is good (one can always revise it from an ac or mol2
> file). Pay attention to atom names since the new version of antechamber
> automatically rename duplicated atom names. The following is the prepin
> file I generated:
>
Just a note: Junmei's prepin file (not shown here) still has duplicate
atom names in the same residue, and so will not work in LEaP. The only
solution I know of right now is to make the atom names unique by hand.
..dac
--
==================================================================
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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