-ins doesn't work as far as I know, and I believe the help text says so. Erik
2 jul 2011 kl. 08.31 skrev Raja Pandian: > Dear All, > > I’m doing research in the field of Protein-DNA interaction. I have gone > through these papers, > A “Solvated Rotamer” Approach to Modeling Water-Mediated Hydrogen Bonds at > Protein–Protein Interfaces > “Effect on DNA relaxation of the single Thr718Ala mutation in human > topoisomerase I: a functional and molecular dynamics study” > “Molecular Dynamics Simulation Study of Interaction between Model Rough > Hydrophobic Surfaces.” > “Prediction of Protein Binding to DNA in the Presence of Water-Mediated > Hydrogen Bonds” > > I have found lot of interesting things on these papers that will be useful > for the progress of my research carrier. > I have been looking for water mediated hydrogen bond in my simulation when i > use g_hbond the -ins option it dose not showing the water mediated hydrogen > bond could you please tell me how to get the hydrogen mediated hydrogen bond > and water mediated free energy in Gromacs ? > Is there any way to calculate water mediated hydrogen bond between > Protein-DNA using Gromacs tools? > If it is possible, please send your program (water mediated hydrogen bond > derivation program) to me and also the program operating procedure. > > Eagerly waiting for your reply. > Thanking You > > Faithfully > Raja > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ----------------------------------------------- Erik Marklund, PhD student 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 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
