Hi Dan,
Thanks for your reply! I tried using autoimage but that doesn't seem to work either. I run into the same problem whether I autoimage before implementing "closest" or after (same as with my original centering/imaging sequence). I still keep getting a trajectory where some of the "closest" waters end up on the wrong side of the unit cell.
-Andrew
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Thursday, December 03, 2015 4:20 PM
To: AMBER Mailing List
Subject: Re: [AMBER] problem with "closest" waters being wrapped
Try replacing all instances of center/image with 'autoimage' - see if
that helps.
-Dan
On Thu, Dec 3, 2015 at 2:17 PM, Kalenkiewicz, Andrew (NIH/NICHD) [F]
<andrew.kalenkiewicz.nih.gov> wrote:
> Dear Amber users,
>
> I've been able to implement the "closest" command in cpptraj to identify and save the water molecules that make up the first and second solvation shells around my solute. Ideally I would like to save these waters (+ solute) to a new trajectory and delete the originals, as I am low on disc space. My problem is that since I used iwrap, waters that were close to the edge of the primary unit cell are wrapped around to the other side. Presumably all the information is there to build a trajectory where this isn't the case and all the waters are in their "actual" positions with respect to the protein. Here is my current sequence of steps in ptraj:
>
> center :1-439 origin mass
> image center origin familiar :1-439
> center :1-712 origin mass
> image center origin familiar :1-712
> center :1-861 origin mass
> image center origin familiar :1-861
> center :1-866 origin mass
> image center origin familiar :1-866
> rms first mass .C,CA,N :1-866
> closest 4500 :1-866 first closestout closestmols.dat outprefix closest
>
> The iterated rounds of centering and imaging were a suggestion I found from the archives to solve a problem with different segments of the solute being out of place. I tried preceding this sequence with "unwrap" but that did not work. Any suggestions would be greatly appreciated.
>
> Thanks,
> Andrew
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Dec 03 2015 - 15:00:03 PST
