On 2010-06-29 03.48, Da-Wei Li wrote:
Hi, all
I recently download the git version and test the CMAP. However, very
strange result I get. I want to use CMAP support in my own
coarse-grained force field.
Basically, I construct a ALA-ALA-ALA system and turn off all energy
terms except bond length, bond angle and CMAP to do some test. The
CMAP is only applied to phi,psi of central residue with a constant
value of -5 (unit is kj/mol, right?) on a 24*24 grid. The result Rama
plot is not a uniformed distribution as expected but avoid 27 regular
distributed region ! (Sorry I can't attach a figure due to size limit).
Can someone help me out?
Maybe the angle potential also implicitly imposes limits to the phi/psi
available space? Try turning it off.
best
dawei
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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