On Tue, 2006-06-20 at 11:31 +1000, Mark Abraham wrote: > [EMAIL PROTECTED] wrote: > > > > Someone has written a script to calculate how may times H2O molecules > > get really close or bind to the N-terminals of a protein?(it's outer > > part, not the core) Or maybe someone nows how to calculate the N-terms > > interactions with the solvent? Anything related to this would help. > > See g_mindist in the manual. >
Or try cvs-version of g_hbond. It has recently been bug fixed in a number of ways and should be able to give you plentiful information about contacts (use -contact flag) and obviously hydrogen bonding (without the -contact option). Depending on the specific information about the interactions you are interested in there are numerous options for g_hbond that may be of interest. /Erik > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 -- Erik Marklund, PhD Student, Molecular Biopcysics group, 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 [EMAIL PROTECTED] _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
