Due to an oversight on my part, 'around' has not been implemented in cpptraj.
However, if you just want to keep track of distances/contacts (rather
than looking for bad overlaps etc) you can either use the 'hbond'
command with '.Cl-' passed to the 'solventdonor' and 'solventacceptor'
keywords, or use the 'nativecontacts' command and give the first mask
as your protein and the second mask as your ions.
Hope this helps,
-Dan
On Fri, May 8, 2015 at 10:39 AM, Aronica, Pietro
<pietro.aronica07.imperial.ac.uk> wrote:
> Yes, I have been looking at that command. My issue is that there is only one mask now. I need to look at a trajectory, and have the program flag how many times does a counterion come close to the protein, perhaps varying the cutoff distance. If I just use the flag .Cl-, it only calculates distances between ions; if I try to expand the mask, it calculates distances between ALL atoms, even the ones I don't want. How can I make it look at contacts between a first mask and a second one, or, more specifically, how do I replicate the around flag of the old checkoverlap?
> Pietro
>
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: 08 May 2015 17:28
> To: AMBER Mailing List
> Subject: Re: [AMBER] cpptraj checkoverlap
>
> On Fri, May 8, 2015 at 12:12 PM, Aronica, Pietro < pietro.aronica07.imperial.ac.uk> wrote:
>
>> Hello,
>> Did something happen to the checkoverlap command in cpptraj? Not only
>> I cannot find it in the manual, but when doing "help checkoverlap"
>> within cpptraj itself it gives the help text for the check command.
>> Did the functionality of searching for close contacts between two
>> masks get transferred to a different command? I can issue the command
>> as I need it to be with an older version of ptraj, but cannot find the
>> equivalent in cpptraj. What am I missing? My cpptraj says it's V15.00b.
>>
>
> Look at the "check" and "checkstructure" commands in cpptraj, which encapsulates what "checkoverlap" does (and adds more checks, I think). See page 559 of the Amber15.pdf manual.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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--
-------------------------
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Department of Medicinal Chemistry
University of Utah
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Received on Fri May 08 2015 - 10:00:04 PDT
