Re: [AMBER] Contacts

From: Sourav Purohit <sour000.gmail.com>
Date: Wed, 20 Aug 2014 19:56:04 +0530

Hi Jason. Thanks. One more quick question.
I used the following command:

contacts byresidue out 2192_2192.dat time 0.02 distance 3 :2192
I get numbers greater than 200 for all frames of the trajectory file.

As far as I understood, this command should calculate the intra-residue
contacts for the all atoms in residue 2192
. This is a lysine residue with some 25 atoms. The number should not be
this large. Is the way I am using the command wrong?? I have attached the
output file.

Thanks.


On Wed, Aug 20, 2014 at 7:28 PM, Jason Swails <jason.swails.gmail.com>
wrote:

> On Wed, 2014-08-20 at 18:44 +0530, Sourav Purohit wrote:
> > Hi Jason,
> >
> > The manual state that "contact" command calculates the contacts between
> all
> > the atoms of the <mask>. I wanted to know whether the same can be done
> > between two masks. Like if I want to calculate the contacts made by atoms
> > in :1-10 only with the atoms belonging to :11-20. If I give :1-20 (as
> only
> > one mask can be specified) as mask, the contact command calculates
> contacts
> > between an atom of residue 1 with that of residue 2 and so on, which I
> > don't want.
>
> Note that I also suggested that you take a look at "nativecontacts".
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Wed Aug 20 2014 - 07:30:03 PDT
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