AMBER Archive (2002)

Subject: Re: transferring structures

From: Matt Hartings (mhartings_at_yahoo.com)
Date: Wed Jun 26 2002 - 15:58:11 CDT

David,
I think that I'm on top of that problem. I think I'm
having troubles with my charged lysine residue. I
don't know exactly what I'm missing, and I don't know
what I should call a charged LYS residue.
Thanks for your help
Matt
--- "David A. Case" <case_at_scripps.edu> wrote:
> On Wed, Jun 26, 2002, Matt Hartings wrote:
>
> > I am currently trying to transfer a peptide
> structure
> > that I generated using a different suite of
> programs
> > to Amber. It seems to be having troubles with the
> > acetyl group. I even have troubles inputing
> structures
> > with acetyl groups directly from programs like
> > HyperChem. The amber prompt gives me errors in the
> > LEap prompt. When I try to loadpdb, it says that
> it my
> > structures have missing atoms which it adds. It
> then
> > will not save the parameters when I use the
> > saveAmberParm command. I have tried some of the
> > tutorials with pdb's from Brookhaven and they seem
> to
> > work out alright. I have even gotten a simple
> > minimization to work out when I use un-acetylated
> > peptides generated with Hyperchem. Its only with
> the
> > acetylated peptides that I am experiencing
> problems.
> > I would greatly appreciate a response. If you need
> > more information from me, please let me know.
>
> What does the beginning (ACE part) of your pdb look
> like? It may be just as
> simple as making sure the atom names match those
> expected by Amber. You can
> check this by giving LEaP the command
>
> desc ACE.1
>
> This will show you the atom names leap is expecting
> to find. "Missing
> atoms" is usually not a problem, but have atoms
> present that leap doesn't
> understand generally is a problem.
>
> ..hope this helps...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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