AMBER Archive (2003)

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

From: GUILLERMINA L ESTIU (gle10_at_psu.edu)
Date: Mon Jul 28 2003 - 11:00:55 CDT

I have fixed it, thanks. It is working now with both amber6 and amber7

On Thu, 24 Jul 2003 21:51:04, "David A. Case" wrote:

> 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
>
> --
>
> ==================================================================
> 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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>
>

Dr Guillermina Estiu
Chemistry Department
Pennsylvania State University
PA 16802

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