[gmx-users] How to avoid adding ions close to ligand

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 26 21:39:01 CET 2012

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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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