On Thu, Nov 01, 2007 at 12:36:33PM +0000, Moutusi Manna wrote: > Hi > I want to perform peptide + popc membrane simulation. I download > popc128a.pdb from > (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies). > Before I introduce the peptide into the membrane, the water layer had to be > broadened to ensure full solvation of the peptide .I increase the water layer > using the following commands > 1. editconf -f popc128a.pdb -o po_box.pdb -box 6.1065 6.1059 9.0000 > -c > 2. genbox -cp po_box.pdb -cs -o po_sol.pdb -p lip.top > > Now, the no. of water molecules over the bilayer increased . But, the > problem is that there are water molecules inside the bilayer, which were > absent incase of popc128a.pdb. How can I remove these offending water > molecules?
calculate the average z position of the phosphorus atoms of both layers, then remove all water molecules - of the just added set! - that lie in between. cheers, marc -- Marc F. Lensink Centre for Structural Biology and Bioinformatics SCMBB Université Libre de Bruxelles [EMAIL PROTECTED] Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium tel: +32 2 650 5411 secr: +32 2 650 2013 fax: +32 2 650 5425 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
