AMBER Archive (2003)

Subject: Re: AMBER: import pdb file in xleap

From: David A. Case (case_at_scripps.edu)
Date: Thu Aug 07 2003 - 16:30:51 CDT

On Fri, Aug 08, 2003, Mi-Kyung Seo wrote:
>
> 1. When I open pdb file which is created by Insight and edit this unit
> (unit editor), the structure contatins only dots, no bonds.
> However, everything is ok with pdb viewer (e.g.VMD)

You need to issue the "bondByDistance" command to get LEaP to put in
bonds using default criteria. VMD is doing the equivalent thing
automatically.

..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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