On 2012-11-26 21:28, Yun Shi wrote:
Hi everyone,
I am doing conventional MD of a protein-ligand system with a mobile
loop as part of the binding site.
Presumably, the positive Arg side chain on the mobile loop will
eventually move towards the negative carboxylic group on my ligand.
But I found the addition of NaCl (0.15 M conc.) had some effect on
this movement, since the random addition could put Na+ or Cl- ions
between the mobile loop and my ligand.
I tried generating a index containing only SOL far not close to my
ligand, but apparently genion requires a continuous solvent group. So
is there any other way to achieve this? Trying different numbers for
-seed option seems inefficient and is dependent on luck.
Thanks,
Yun
Maybe your assumption is wrong?
Run a long MD simulation and you will find out.
--
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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