Hi,
You should try using the "noimage" keyword with the closest command; I think that should do what you want.
Marc
Sent from my iPhone
> On 3 Dec 2015, at 22:34, "Kalenkiewicz, Andrew (NIH/NICHD) [F]" <andrew.kalenkiewicz.nih.gov> wrote:
>
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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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>
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Received on Thu Dec 03 2015 - 15:00:05 PST
