[gmx-users] solvent molecules between protein-peptide complex

[Anton Feenstra]

Marc F. Lensink wrote:

> On Mon, Apr 18, 2005 at 03:54:45PM +0530, Alok wrote:
> 
>>hello gromax users,
>>                              I have simulated a protein-peptide 
>>complex solvated in water.
>>Now i want to specifically analyse the number of solvent molecules 
>>between the protein-peptide complex as a function of time.
>>Is there any direct or indirect tool available in GROMACS to help me 
>>carry out this analysis.
>>Please suggest some solution.
>>Thanking you all in advance.
> 
> 
> i have a tool that may do what you want.  i've used it for
> peptide/lipid interaction, to define the lipids that are under the
> peptide.  as in a membrane simulation the normal to the bilayer is
> typically the z-axis, you'll have to rotate your system to conform to
> this convention.  i think you can do that by using editconf to
> generate one such structure, and then with trjconv you fit all frames
> to that reference structure.  contact me off-list if you want to get
> the source of the program.

You may as well get around by using g_hbond. Although it is desinged for 
H-bond detection, it could easily be modified (in the source code, that 
is) to look at any type of close contacts.


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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