AMBER Archive (2003)

Subject: Re: AMBER: strange problem with a small system

From: David A. Case (case_at_scripps.edu)
Date: Thu Jul 24 2003 - 23:51:04 CDT

On Wed, Jul 23, 2003, GUILLERMINA L ESTIU wrote:

> I am attaching the log file.
> Amber6 works for the system

Thanks, but I wonder if you can help more, by trying to isolate this down
to a simpler case? You seem to be loading lots of molecules, sourcing files
we don't have, and so on, so it's not readily possible to try to reproduce the
problem.

I note that you are reading in an unknown residue, allowing LEaP to create new
atoms, then trying to "set" all of the parameters in a LEaP script. I would
ordinarily create a new unit, save it to an off file, then read that back in
before loading in the final PDB file (so that there are no missing atoms, etc
at that point.) We should still try to track down your problem, but going the
alternative way might help as well.

..regards...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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