Re: [AMBER] cpptraj checkoverlap

From: Daniel Roe <>
Date: Fri, 8 May 2015 10:51:00 -0600

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,


On Fri, May 8, 2015 at 10:39 AM, Aronica, Pietro
<> 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 []
> 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 <> 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
> _______________________________________________
> AMBER mailing list
> _______________________________________________
> 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)
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Received on Fri May 08 2015 - 10:00:04 PDT
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