From: Vani Krishna (vakri2002_at_yahoo.com)
Date: Mon Aug 02 2004 - 10:11:48 CDT
I have sent this question earlier, and got no replies.
I am in the process of parameterizing a new molecule,
and Iam confused about how to specify the torsionla
parameters (i have the barrier).
When i was going through the NAMD code, The torsion
(K) is multiplied by some 'scale' factor. What is this
factor? Does this depend on the number of bonds
to rephrase, if i want to know the absolute barrier
from the 'K' values in CHARMM format, should I
multiply by some factor? if so what is it?
Iam guessing it is (2 x maximum torsions about the
bond). e.g X-C=C-X, it would be 2 x 4 =8
Is this right? otherwise some of the K's for peptide
bonds seem too low (O C NH1 CT1 2.5000
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