[gmx-users] Regarding membrane protein solvation

Alan Dodd anoddlad at yahoo.com
Fri Jun 1 10:28:37 CEST 2007


Check the manual for 'genbox'.  Once you work out how to use it, remember to check your output for waters within the bilayer - I'm not sure how big the cavities are, but I wouldn't be surprised if you could fit a water molecule or two in.

----- Original Message ----
From: naga raju <nagaraju_cy at yahoo.co.in>
To: gmx-users at gromacs.org
Sent: Friday, June 1, 2007 8:07:08 AM
Subject: [gmx-users] Regarding membrane protein solvation


Dear gmx users,
                I inserted mebrane protein in DOPC
lipid bilayer, some part of protein is outside of
lipid bilayer. Would you tell me how to add water
molecules to protein(to the out side of lipid bilayer
part) around 6 angstroms radius.    
        any suggestion is appreciated.
                      
                                  with best regards,
                                    Nagaraja.



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