Re: [AMBER] nativecontacts

From: Gustavo Seabra <>
Date: Wed, 29 Apr 2020 08:56:19 -0400


I had this situation before, with contacts output from Chimera. The
solution I found was to write an AWK script that would count the
interactions for each residue from the Chimera output. The advantage of AWK
there is that you can use strings as array indexes, such that when you
encounter "ASP9" you can create a variable like counter["ASP9"], and just
increase its counter by 1, for example, making it easy to use it to count
the interactions.

Take a look at the attached file. You will probably need to modify it to
adapt for your case, but it may be a start.

I hope that helps,
Gustavo Seabra.
On Wed, Apr 29, 2020 at 2:35 AM mohamed marzouk <> wrote:
> Hello everyone;
> I want to know the contact residues between protein and DNA in complex at
> 5A as example, so it’s easy to use nativecontacts  function in  cpptraj.
> However I want to know only the residue of contacts without repeat for
> every atom.
> To indicate by example
> I need to get residues from DNA are 2,4,6,78,89 and so on, but the out put
> may write residue 4 for 6 times due to 6 different atoms from 4th residue
> make 6 contacts with residue from protein I am not interesting in this
> repeatation.
> How can I get this desired contacts for residues without repeat for every
> atom???
> Best regards,
> Mohamed Marzouk Sobeh
> Ph.D student at Life Science and Technology, Tokyo Institute of
> Technology, Tokyo, Japan.
> T.A Physics department,Ain Shams University, Cairo, Egypt.
> Emails:
> Mob. and WhatsApp.:
>                +81 070-4070-9549
>                 +2 01061417414
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Received on Wed Apr 29 2020 - 06:00:03 PDT
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