Re: [AMBER] Tracking lifetime distance by closest of specific water IDs?

From: Daniel Roe <>
Date: Tue, 4 Aug 2020 09:28:49 -0400


So I'm not 100% clear on what you're trying to do, but if all you want
to do is track certain waters, why doesn't identifying potential
waters with 'closest' work, then strip the waters you find there. The
output from 'closestout' has both the molecule number and the first
atom number of each water, so you could potentially use that to
determine which waters to keep. Apologies that I'm not quite getting
what you want - hope this maybe helps a bit.


On Tue, Jul 28, 2020 at 10:29 AM Kenneth Huang
<> wrote:
> Hi all,
> I have an odd scenerio where I'm trying to track the full distance lifetime
> of a subset of waters from an initial time point, ie frame 1, from a group
> of bases over 25 ns chunks of time. I'm having an issue in tracking all the
> waters though, in that if I use something like
> closest 17130 :8-10&!(.H=) noimage first closestout closest_s2_200
> outprefix closest_s2
> Where I have a total of 17131 waters in my box, but the problem I'm running
> into is that a number of those waters move so far away they're the
> furtherest water, so aren't recorded.
> I tried stripping out the all but the waters I'm interested in, but I ran
> into two issue where I couldn't tell if it was actually leaving the right
> waters, and my input for closest has it as N=total number of waters in the
> box.
> If it were just one residue, I'd try something with distance to get the
> missing distance like
> dist :WATID.O :8.CA out waterid_8ca.out
> And just take the min distance of the atoms in the group. But given there's
> three bases, the number of atoms to the water gets large. Given that, I
> feel like there's a simple solution that I'm just not thinking of?
> Best,
> Kenneth
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
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Received on Tue Aug 04 2020 - 06:30:02 PDT
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