[gmx-users] question about number of atomic contacts beetween residues

[Leonardo Sepulveda]

Thanks a lot, Anton. I will try to change the g_mdmat code with a
friend. If it is acomplished i`ll send the code to you. Mi
"calculations" is the "fraction of contacts (Q) " very used in protein
folding. I have read that the standard way to do that is calculate the
Van der Walls radii of each atom plus 0.5 angstroms. If the radii
(defined in that way) of two atoms overlap, then a contact exist.
Nevertheless i read in the mindist program (Patricia Soto told me it
calculate contacts too) that the way to define the radii is giving a
cutoff (default 6 angtroms) for each atom. Does g_mdmat calculate
contacts acording to a predefined cutoff or it does acoording to the
force field van der walls radii of each atom?
The paper where i read that metod used CHARMM, so is easy because it
have all the atoms. How  can be done for a united atom FF like
GROMOS96?? i am confused about it.

Leonardo Sepúlveda


On Mon, 29 Nov 2004 18:07:12 +0100, Anton Feenstra <feenstra at few.vu.nl> wrote:
> Leonardo Sepulveda wrote:
> 
> 
> 
> > Hello list!!!
> >
> > I want to calculate, for each frame of the dynamics of a protein, the
> > number of atomic contacts beetween every residue of it. I tryed with
> > g_mdmat, with the following line
> >
> > g_mdmat -f traj.trr -s ini.tpr -frames -no
> >
> > nevertheless, -no give me the numeric average contacts in num.xvg, and
> > -frames gives me a plotable dmf.xpm for every frame. what I need is
> > the matrix of number of contacts represented in dmf.xpm but in numeric
> > format, to make some calculations. There is a special option in
> > g_mdmat or another program to acomplish that???
> 
> no. It won't be difficult to put it in - if you know a bit of c.
> Alternatively, you can put the code for your 'some calculations' into
> g_mdmat itself.
> 
> --
> Groetjes,
> 
> Anton
>  _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> |             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
> |             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
> |_____________|_______________________________________________________|
> 
> 


-- 
Leonardo A. Sepúlveda Durán
Bioquímico