AMBER Archive (2002)

Subject: Re: example 1 problems

From: David A. Case (case_at_scripps.edu)
Date: Tue Sep 17 2002 - 09:45:31 CDT

On Tue, Sep 17, 2002, Alicia Hopkins wrote:
> >
> > Example 1 is from Amber 6, specifically titled Minimization of BPTI in
> vacuum.

Thanks. You should be aware that there have been some changes between
Amber 6 and 7, so that running Amber7 using Amber 6 demos might cause
problems.

> When I specify the leaprc location in the search path; must I do this
> every time I invoke teLeap? Surely there is a shortcut!

You could alias "tleap" to "tleap -f leaprc.ff94" (or similar).

> The leap.log file lives in the test directory; I think this is a problem
> too, how should I go about fixing this?
>

The location (and name) of the log file is specified in the leaprc file.
These generally point to the current directory and name the file "leap.log".
Just edit your leaprc file to get different behavior.

..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
==================================================================