Dear AMBER,
I am setting up AMBER simulations of a proteins containing zinc fingers,
and I am trying to use the Zinc parameters from Yuan-Ping Pang, together
with the library and parameters downloaded from the website given on the
AMBER homepage:
http://www.mayo.edu/research/labs/computer-aided-molecular-design/projects/zinc-protein-simulations-using-cationic-dummy-atom-cada-approach
When I try to save AMBER parm files I am getting messages like:
1-4: angle 43748 43749 duplicates bond ('triangular' bond) or angle
('square' bond)
Is this anything to worry about?
One other thing bothered me a little bit - when I try to solvate the system
I get messages like:
(using default radius 1.500000 for D4)
(using default radius 1.500000 for D3)
(using default radius 1.500000 for D2)
(using default radius 1.500000 for D1)
I suppose this is not important, but I wanted to confirm this with you.
Thanks in advance,
Holly
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Received on Mon Dec 02 2013 - 17:00:03 PST
