Re: Brief courses on AMBER 6

From: David Case <>
Date: Wed 30 Aug 2000 09:48:16 -0700

On Wed, Aug 30, 2000, Michael Cooney wrote:

> I am the postdoc at UGA who joined the Reflector yesterday.
> Presently I am trying to set up a complicated protein:DNA
> complex in AMBER 6 using LEAP and am having various difficulties
> mainly with atom names. I wondered if there are any short hands-on
> courses for new users of AMBER 6 offered any time soon, preferably
> in the Southeast but I would consider anywhere in the USA. At this
> point I am just inquiring, as I would have to ask whether my department
> could pay for tuition and travel. While the manual is very helpful,
> there is no substitute for hands-on training.

I don't know of any courses. Be sure to check out the tutorials on the
web page. Two of these have been recently completely revised, and should
help you get through many problems.

The "general" key to getting LEaP to work is to keep editing your starting
PDB file until LEaP stops complaining about atom names. The names that
Amber uses in its libraries can be found in the *.in files in the dat
subdirectory. It is very common to have to manually edit incoming pdb
files to get everything to match.

...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 Wed Aug 30 2000 - 09:48:16 PDT
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