Re: AMBER pdb help - lost atoms - Part 2

From: David A. Case <>
Date: Thu, 3 Apr 2003 09:23:41 -0800

On Thu, Apr 03, 2003, wrote:

> Thanks for the responses on my first post. I've tried even more methods to
> get my pdb file to be completely read in, but even starting with nukit,
> then nucgen, then leap or antechamber doesn't seem to work.

Sorry, my memory of your problem is not what you think it is. Saying
"leap or antechamber doesn't seem to work" doesn't help enough. Exactly
what commands did you give, and what was the result?

> And leap
> insists on adding the sugar and phosphate to each base, and I am not using
> them in my study.

If you want to use the standard libraries for nucleic acids, then LEaP
will indeed add atoms that it needs to get that standard moiety. If you
want to model something that is not in the standard library, you need to
make your own templates. You can do this by editing an existing template
(change the residue name to avoid confusion with the standard names), or
use antechamber to build the template for you.

..good luck...dac

David A. Case                     |  e-mail:
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            |
Received on Thu Apr 03 2003 - 18:53:01 PST
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