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AMBER Archive (2006)Subject: AMBER: AMBER 8 - dihedral angles when clambda=1
From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Dear amber users/developers,
I am doing free energy calculations using the TI Approach. Here is a
cytidine isocytidine
C6 - C5 H41 C6 - C5 DH41
I have set the dihedral parameters of the dummy atoms (the ones with DH..)
DH-O -C -N* 1 0.00 180.0 2. [X -CA-N2-X]
These are the necessary dihedral parameters for the dummy atoms (I have
When I do a minimization using icfe=1, klambda=6, clambda=0; at the
When I do a minimization using icfe=1, klambda=6, clambda=1; at the end, I
When clambda=1, that means that the structure is 'isocytidine'. And having
I would like to hear your ideas on what I might be doing wrong here.
Best,
-- Ilyas Yildirim --------------------------------------------------------------- - Department of Chemisty - - - University of Rochester - - - Hutchison Hall, # B10 - - - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) - - http://www.pas.rochester.edu/~yildirim/ - ---------------------------------------------------------------
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