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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 19 2011 - 13:30:04 PST
