Re: [AMBER] nativecontacts in ambertools14

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 11 Nov 2014 12:55:40 -0700

Hi,

The documentation in this case is not as clear as it should be (mea
culpa). There are two things going on here. The first is that the
normalization factor that is actually used is the number of frames, so
when you are calculating the map by atom (the default) a value of 1.0
indicates the contact is present for every frame. However, if you are
going by residue ('byres') there are multiple atoms that can make
contacts between two residues, so the actual number for each contact
varies depending on how many selected atoms are present in each
residue. Say for example you have two simple residues, one with 4
atoms and the other with 3. If all atoms in both residues are selected
there are 12 potential contacts, so the max value for that residue
contact pair is 12. My reasoning behind this was to reflect the fact
that larger residues do have the potential to form more contacts.

The second thing that is going on is that when a non-native contact is
formed it is given a negative value instead of a positive one.

Hope this helps, sorry for the confusion,

-Dan


On Tue, Nov 11, 2014 at 10:03 AM, Asmita Gupta <asmita4des.gmail.com> wrote:
> Dear users,
>
>
> I am calculating contacts between a protein-protein complex in a
> trajectory using nativecontacts command from ambertools14. In the manual,
> it has been specified that the map file written has values normalized to
> 1.0 (can i assume it is from 0 to 1 depending on their lifetime occurrence
> during trajectory??)
>
> i have used this command:
>
> nativecontacts :1-974 :976-1143 writecontacts p1_p2_contacts.dat distance
> 5.0 out p1_p2_cont_num.dat first name p1-p2 byresidue map mapout
> p1_p2_map.dat
>
> in the map file, i am getting some values which are negative, and some are
> way beyond 1.0..like-
>
> ===============
> 805.000 1095.000 -0.0525
> 808.000 1095.000 -2.5484
> 851.000 1095.000 -1.6074
> 852.000 1095.000 -1.0348
> 853.000 1095.000 -22.9172
> 854.000 1095.000 -0.0344
> 856.000 1095.000 -0.0190
> 904.000 1095.000 -1.9920
> ...
> ...
> ...
> 796.000 1143.000 13.4246
> 797.000 1143.000 8.0078
> 798.000 1143.000 1.6831
> 799.000 1143.000 2.3897
> ==================
>
>
> I don't think these are normalized values and why negative values are
> coming?? Can you please explain what's going wrong here..
>
> Thanks
>
> Asmita
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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 Tue Nov 11 2014 - 12:00:03 PST
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