Re: [AMBER] cpptraj checkoverlap

From: Aronica, Pietro <>
Date: Fri, 8 May 2015 16:39:42 +0000

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?

-----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.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
AMBER mailing list
Received on Fri May 08 2015 - 10:00:03 PDT
Custom Search