AMBER Archive (2000)

Subject: Re:

From: Jarrod Smith (jsmith_at_chazin.structbio.vanderbilt.edu)
Date: Tue Apr 04 2000 - 10:30:23 CDT

jramon_at_husky.bq.ub.es wrote:
> I would appreciate annyone who can give me a solution. HOW CAN I SAY TO XLEAP THAT IT HAS TO LOOK FOR THE NEW SPECIFIED RESIDUE IN THE LIBRARY THAT I HAVE PREVIOUSLY LOADED????
> Thanks a lot for your answers,
> Bals

I didn't quite follow everything that you tried, but in general, to
define a new residue with LEaP:

1. load the coordinates for the new residue into leap with loadpdb:
> T3M = loadpdb T3M.pdb

2. Explicitly set the unit and residue names of the unit:
> set T3M $name $T3M
> set T3M.1 $name $T3M

3. Edit the residue, enter draw mode, and add missing bonds. Select the
residue, go to EDIT->EDIT SELECTED ATOMS to add atom types, partial
charges, etc. Be careful not to accidently create new atoms if you are
trying to bond existing atoms with the mouse:
> edit T3M

4. Check the residue, and add any missing forcefield parameters that are
a result of new combinations of atoms types:
> check T3M

5. Save your work:
> saveoff T3M T3M.off

If you wanted to start with thymine and go from there, it could save you
some work, but the same basic steps should be followed. Start with THY,
change the unit and residue names, edit the residue to your spec, check
the residue and add missing parameters. Then load T3M.off with the rest
of your libraries and everything should work OK. Check the addpdbresmap
command if you want to automate translating pdb residue names to leap
residue names.

Hope that helps. 

-- 
Jarrod A. Smith, Ph.D.
Assistant Director, Center for Structural Biology
Molecular Graphics and Computation
Vanderbilt University

jsmith_at_structbio.vanderbilt.edu