Thanks.
On Wed, Aug 20, 2014 at 8:53 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> The way the 'contacts' counts contacts, the total number of contacts
> is multiplied by two, i.e. A->B and B->A are each counted separately.
> Therefore the actual number of unique pairs is more like ~100, which
> seems fine for a residue the size of lysine. The 'nativecontacts'
> command on the other hand only counts unique contacts, so it will in
> general be half as big as the numbers reported by 'contacts'.
>
> Hope this helps,
>
> -Dan
>
> On Wed, Aug 20, 2014 at 8:26 AM, Sourav Purohit <sour000.gmail.com> wrote:
> > 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
> >>
> >>
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
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Received on Wed Aug 20 2014 - 10:00:03 PDT
