Hi,
I read the tutorial that's "Thermodynamic Integration using soft core
potentials <
http://ambermd.org/tutorials/advanced/tutorial9/index.html>" on
the web site of amber. But I cannot understand the process completely. Now
I want to modeling the water contribution to the ligand-binding affinity by
the double decoupling method. How should I apply the principle in your
tutorial? I wonder if the icfe parameter should be set from minimization
mdin to equilibrium mdin and if the water should be constraint at the
binding site by a constraint force as described in the literature from
http://pubs.acs.org/doi/abs/10.1021/ja0377908. As well, I cannot use the
pmemd method to run Thermodynamic
Integration<
http://ambermd.org/tutorials/advanced/tutorial9/index.html>
<
http://ambermd.org/tutorials/advanced/tutorial9/index.html>simulation.
Another question is about the sander.
My command is "sander -ng 2 -groupfiles 《Mygroupfiles》"
the erro is "mdfil: Error unknown flag: -ng" but the recommended
parameters include the -ng flag. I used amber10.
I am much looking forward to help.
--
PhD Ting Ran
CPU(CHINA PHARMACEUTICAL UNIVERSITY)
Molecular-Design & Drug-Discovery Lab
Laboratory Building A212
639 Longmian Avenue
Nanjing, 210009
P.R.China
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Received on Sun Sep 29 2013 - 19:30:04 PDT
