Re: [AMBER] problem with "closest" waters being wrapped

From: Kalenkiewicz, Andrew (NIH/NICHD) [F] <"Kalenkiewicz,>
Date: Thu, 3 Dec 2015 22:34:59 +0000

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.

From: Daniel Roe []
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.


On Thu, Dec 3, 2015 at 2:17 PM, Kalenkiewicz, Andrew (NIH/NICHD) [F]
<> 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
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
AMBER mailing list
Received on Thu Dec 03 2015 - 15:00:03 PST
Custom Search