[gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule
erikm at xray.bmc.uu.se
Sat Mar 17 14:36:27 CET 2007
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.
17 mar 2007 kl. 11.17 skrev OZGE ENGIN:
> 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
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