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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Received on Fri May 08 2015 - 10:00:03 PDT
