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 - 08:30:02 PDT
