Hi,
I think maybe you can do what you want with cpptraj's 'nativecontacts'
command. Make sure you're using the latest version. One mask would be
protein, the other mask would be probe molecules. Specify
skipnonnative to make every contact non-native, and track the
residences with '[savenonnative [seriesnnout <file>]' etc.
Hope this at least begins to help,
-Dan
On Mon, Mar 25, 2019 at 10:58 AM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
>
> Hi All,
>
> I think I am confused and would appreciate any help from you guys in case you have an idea as to how to go about it.
> I have a protein(3KFA) and I have it soaked in water+acetonitrile, water+imidazole , water+ ethanol, water+methanol, and water+ pyrimidine.
>
> Approx I have 100 probes mixed in ~3300 water molecules.
>
> Now I have mapped the regions of the protein where is favorable binding of these probes listed above.
>
> I need to calculate the distance between the mapped hotspot x,y,z coordinates (Center of mass) and the probe molecule to get a residence time for the probe in that spot.
> But in my case I have certain hotspots which house more than 1 probe at the same time!
> Now, if I want to calculate the distance between the active site (COM co ordinates) and the probe how to achieve it?
> Like how to label which prob (out of 100 probe molecules) have resided in my active sites?
>
> I need to calculate the distance time series in my trajectory of 80000 snapshots
>
> Thanks
> Debarati
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Received on Tue Mar 26 2019 - 12:30:02 PDT
