Re: [AMBER] CPPTRAJ contacts and nativecontacts

From: PAQUET Amaury <>
Date: Tue, 31 Jul 2018 11:11:52 +0000

Thank you for your help, after trying your suggestion with ambertools18, I obtained exactly what I needed

-----Message d'origine-----
De : Wesley Michael Botello-Smith []
Envoyé : vendredi 27 juillet 2018 17:48
À : AMBER Mailing List <>
Objet : Re: [AMBER] CPPTRAJ contacts and nativecontacts

After looking through our old versions of amber, it looks like you may need to use ambertools 15 or later to get series output from nativecontacts.

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 DMRC/SPDS/LILA
> Bat 181 France<>
> 00 33 4 66 79 55 17
> _______________________________________________
> AMBER mailing list
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Received on Tue Jul 31 2018 - 04:30:03 PDT
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