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
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu