AMBER: parmbsc0

From: Dr. Suzie Byun <byun.bu.edu>
Date: Sat, 19 Jul 2008 11:40:05 -0400

Hello,
I had an Amber related question regarding the parmbsc0 force field.
When I use tleap to make my dna 20-mer duplex using the directions on
your webpage:
http://mmb.pcb.ub.es/PARMBSC0/README.txt

I get the following warning message for improper torsion parameters
including these:

Building improper torsion parameters.
    ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
           atoms are: N9 C5 C4 N3
    ** Warning: No sp2 improper torsion term for NB-CA-CB-CB
           atoms are: N7 C6 C5 C4
    ** Warning: No sp2 improper torsion term for OH-H1-CI-H1
           atoms are: O5' H5'1 C5' H5'2


How can I fix this problem? Thanks very much.

Suzie Byun 


-- 
Dr. Suzie Byun
Postdoctoral Faculty Fellow
Boston University
Department of Chemistry
590 Commonwealth Avenue
Boston, MA 02215
----- End forwarded message -----
-- 
Dr. Suzie Byun
Postdoctoral Faculty Fellow
Boston University
Department of Chemistry
590 Commonwealth Avenue
Boston, MA 02215
----- End forwarded message -----
-- 
Dr. Suzie Byun
Postdoctoral Faculty Fellow
Boston University
Department of Chemistry
590 Commonwealth Avenue
Boston, MA 02215
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Received on Sun Jul 20 2008 - 06:07:58 PDT
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