Re: [AMBER] how to add new groups to all_amino94.in

From: Jason Swails <jason.swails.gmail.com>
Date: Sat, 19 Nov 2011 16:26:15 -0500

On Fri, Nov 18, 2011 at 12:20 PM, Li, Yawen (MU-Student) <
yl6c2.mail.missouri.edu> wrote:

> Hi, all.
>
> I am running the AMBER program which is installed on a university server.
> I do not have the authority to edit the all_amino94.in file. However,
> since the molecule I want to study has some non-standard amino acid
> functional groups. I have to be able to include parameters in the library,
> in order to set up the coordinate and parameter files correctly in the
> first place.
>
> Does anyone know how to tell LEaP to read functional group parameters from
> a working directory?
>
> Thank you for any help in advance,
> Yawen Li
>

The "loadOFF" command in leap allows you to load any library files you have
laying around. The directories that are searched for the library files are
$AMBERHOME/dat/leap/lib as well as the current working directory. You can
add more directories to your search path via the -I flag to tleap. That is,

tleap -I/path/to/my/libs

If you don't already have the library files generated, then see the
tutorials or Francois' advice regarding how to create them.

HTH,
Jason


> Graduate student
> Chemistry Department
> University of Missouri-Columbia
> Email: yl6c2.mail.missouri.edu
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-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Nov 19 2011 - 13:30:04 PST
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