Re: [AMBER] CPPTRAJ contacts and nativecontacts

From: Wesley Michael Botello-Smith <>
Date: Fri, 27 Jul 2018 08:41:22 -0700

I am using v17.00 right now, but I believe v14 is equivalent for this
purpose. I have done more or less what you are doing myself. You need to
use the 'series' and 'seriesout <file>' and 'seriesnnout <file>' options to
get timeseries data to be written.
The time series data will then contain one column for every residue pair
and one line for each timestep, with the first column corresponding to
frame number. The seriesout file is for native contact series and the
seriesnnout file is for non-native time series.
Hope that helps...

-Dr. Wesley Botello-Smith

On Fri, Jul 27, 2018 at 7:16 AM, PAQUET Amaury <> wrote:

> Dears Amber users,
> I would ask for your help for using CPPTRAJ contacts and nativecontacts
> for a specific purpose. I am using CPPTRAJ V14.25
> I am currently using the "contacts" command with the "byresidue" option in
> order to obtain an output file where each residue is in one column and each
> line corresponds to one step. So I can have, for each residue, its number
> of contact for each step and then calculate its average number of contact
> on the entire trajectory. Then doing it for all the residue allow me to
> calculate, for the entire trajectory, the percentage of residue with 0, 1,
> 2 etc.. contacts.
> The command line that I use is :
> contacts byresidue out filename distance 8.0 @%OS (OS is the atom type of
> interest in the residue)
> But now I would like to do the same thing but between two different atom
> types (OS and OH). I tried to use for that the command "nativecontacts"
> for its possibility to calculate contacts between two masks. I tried to use
> this command line :
> nativecontacts .%OS .%OH distance 8.0 contact.out byresidue map mapout
> map.out
> The contact.out file contains only for each step the number of native and
> non-native contacts and the map.out file contains the normalized number of
> contact between each residue and I'm not interested in these data. Is there
> a possibility to obtain an output file like with the "contact" command with
> residues in column and the line corresponding with the number of contact
> for each step?
> I also tried to do that with the "contacts" command and the two atom types
> in the mask :
> contacts byresidue out filename distance 8.0 @%OS,OH
> but I just obtained the contacts between OS-OS atom types and between
> OH-OH and not the one I'm looking for which is between OS-OH atom types
> I hope my request and english are clear and comprehensible.
> Thank you for your help
> Amaury Paquet
> Doctorant 3ème année/3rd year PhD student
> CEA Marcoule
> Bat 181
> France
> 00 33 4 66 79 55 17
> _______________________________________________
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Received on Fri Jul 27 2018 - 09:00:02 PDT
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