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

[Anton Feenstra]

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)    |
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