From: Vani Krishna (vakri2002_at_yahoo.com)
Date: Mon Aug 02 2004 - 10:11:48 CDT
Dear all:
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
shared?
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
Kcal/mol)
Thanks
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