[gmx-developers] Making personal plugin

[Anton Feenstra]

Jonathan Khao wrote:
> Anton Feenstra a écrit :
> Thank you for your responses. Effectively , I haven't been clear on what 
> we intend to do.  My system is a Protein Detergent Complex, and our goal 
> is to know how atoms behave are along the faces of an alpha helix. So we 
> wanted to make a tool that read a Trr file, and converted the 
> coordinates  as a function of :
>        - the position along the axis of the protein ( fitted to the Z 
> axis )
>        - the distance from the axis
>        - and an angle
> So correct if I'm wrong, as you suggested, the use of gromacs's 
> functions to read the "trr" trajectory is not worth it, a custom made 
> tool should therefore be more appropriate ? If so are there any 
> instructions on how to "decrypt" the "trr"  files ?

There is somewhere a template tool (template.c IIRC) that is basically 
an empty program that just reads coordinates from your trajectory. That 
should get you started.

Also, there is at least one tool that is specific for the analysis of 
helices, IIRC it can do axis fitting.

> I've also been working on an other project for some time. I wanted to 
> get properties of some molecules (detergents) which are in the vicinity 
> of my alpha helix. The properties that I want to get are avaliable using 
> the gromacs tools. But where I need help, is in the selection of the 
> molecules in the "vicinity".
> 
> I've done verry heavy programming scripts which computes the distances 
> of each molecules ( degergents ) with the g_mindist , then i read each 
> of the "xvg" files , got the intervals where it was under the cutoff 
> value, made sub trajectories, concatenated them and then applyed the 
> gromacs tools. I suppose there are easy shortcuts to follow , especially 
> by avoiding the time spending printing and reading parts.
> So could you help me by  telling me how i could apply a filter on the 
> tools ? It would be verry usefull, and would at last help me to dive in 
> the gromacs source code.

I'd suggest modifying g_mindist to suit your needs. It's been a while 
since I been through that code, so I'm not sure how easy it is to read it.

Another tool you might want to use for this, is g_hbond. Although it is 
developed for H-bonds, with the proper setting of angle- and distance 
cutoffs, and donor and acceptor atom/types, you should be able to get 
more general info on solvent/detergent vicinity. Plus, g_hbond is 
reasonably optimized for large-scale pairwise distance calculations (it 
uses neighboursearching).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Free University  Amsterdam     |
|(   |   )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands  |
| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You Want Something Done You Have to Do It         |
|             | Yourself" (Highlander II)                             |
|_____________|_______________________________________________________|