You'd have to add the angle calculations and add them to 'filter'.
This will all be much easier once I add support for bridge time series
data sets.
On Tue, Jul 3, 2018 at 1:16 PM, Kenneth Huang <khuang8.student.gsu.edu> wrote:
> Yeah, I think the problem is the angle part- if I up the number of waters that closest records between two residues, then it picks up on the right waters in the mass. I don't suppose there's a way to filter out angles in closest, or would I have to just filter out later down the road with filter?
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Tuesday, July 3, 2018 8:38 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Individual bridging water lifetimes by closest?
>
> On Mon, Jul 2, 2018 at 4:18 PM, Kenneth Huang <khuang8.student.gsu.edu> wrote:
>> Thanks for the pointers- it does sort of works for my system, but it does seem to get thrown off every once in a while in picking waters by the geometric center. I'll keep fiddling with it to see if I can't get it to work properly. Is there a way for hbond to print out the atoms that are getting bridged along with the molecule?
>
> Yes, use the 'bridgebyatom' keyword. Another thing to keep in mind is
> that by default 'hbond' uses an angle criterion in addition to
> distance, while the script I gave you is distance only. Maybe that
> accounts for some of the discrepancy?
>
>> Also, am I correct in assuming that using the center keyword with closest makes it use the geometric center vs the center of mass that distance uses?
>
> Not exactly. When 'center' is specified, 'closest' will determine the
> closest solvent molecules to the geometric center of the atoms in
> <mask>. When not specified (i.e. the default behavior) 'closest' will
> determine the closest solvent molecules to *any* atom in <mask>. The
> latter behavior is useful for when you want something like a solvation
> shell around your solute.
>
> -Dan
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%7Ckhuang8%40student.gsu.edu%7C8041401fe5c743a32eb608d5e0e20198%7C704d822c358a47849a1649e20b75f941%7C0%7C0%7C636662183645496506&sdata=I2dZndjXdnKJLOPBL0k3o3VOLRchJPUDJKQRpspXOwk%3D&reserved=0
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 03 2018 - 10:30:03 PDT
