[gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule

[Erik Marklund]

Hi. g_hbond can do that, sort of. You can calculate e.g. the nr of  
water oxygens within a certain distance from the protein. The  
limitation lies in that g_hbond operates at a atom basis, not  
molecule, meaning that there is strictly no way of finding the number  
of solvent molecules directly. However, I think that counting the nr  
of water oxygens would be good enough for most applications.

/Erik

17 mar 2007 kl. 11.17 skrev OZGE ENGIN:

> Hi,
>
> I want to calculate the number of solvent molecules within a cutoff  
> distance around the protein molecule. I could not find the  
> appropriate command for this in manual. Moreover, I could not  
> understand the information for g_sorient.Could you give me a more  
> detailed explanation for this?
>
> Thanks in advance
>
> Ozge Engin
>
>
>
>
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys