Hi,
To change the definition of 'solvent' for the 'closest' command,
please use the 'solvent' command just prior:
solvent <new solvent mask>
closest ...
Hope this helps,
-Dan
On Fri, Mar 22, 2019 at 3:23 PM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
>
> Hi All,
>
> I am trying to replicate some ideas given in https://doi.org/10.1002/cmdc.201100237
>
> [cid:3e994689-347c-4066-94a1-417766f31335]
> I have a protein in a water+acetonitrile co solvent box and I am trying to get the time series distance to be spitted out between the center of mass coordinates of the active site and the closest acetonitrile molecule. My system has 100 acetonitrile molecules and 3000 TIP3P waters.
> I have 4 plausible binding sites and I need to get a similar graph as this one to compute the distance between the closest acetonitrile and the binding site.
>
> Any ideas will be very helpful; as I found out the closest seems to identify water as solvent!
> Thanks
> Debarati
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Received on Fri Mar 22 2019 - 13:00:02 PDT
