[gmx-users] % of existence of hydrogen bond
Dear all, I am dealing with a POPC+PEPTDE+WATER system. Basic residues of the peptide make hydrogen bonds with lipid headgroup (as reflected from g_rdf analysis) and the number of hydrogen bonds formed can be calculated from g_hbond program. Now, i want to calculate the % of trajectory time for which a bond between a particular group (say LYS and lipid headgroup po4) exist. -hbm gives a .xpm matrix, on solving (using xpm2ps) that i got a .eps file, which is a picture file of h_bond existence map, but the data sheet is not given. Can any one help me to solve this problem? With regards, Moutusi Manna Now, send attachments up to 25MB with Yahoo! India Mail. Learn how. http://in.overview.mail.yahoo.com/photos___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] % of existence of hydrogen bond
Hi, You can use g_hbond -num and write a small script to calculate the percentage of h-bond existence per frame by calculating the number of frames for which a h-bond exists. Good luck, Ran. Moutusi Manna wrote: Dear all, I am dealing with a POPC+PEPTDE+WATER system. Basic residues of the peptide make hydrogen bonds with lipid headgroup (as reflected from g_rdf analysis) and the number of hydrogen bonds formed can be calculated from g_hbond program. Now, i want to calculate the % of trajectory time for which a bond between a particular group (say LYS and lipid headgroup po4) exist. -hbm gives a .xpm matrix, on solving (using xpm2ps) that i got a .eps file, which is a picture file of h_bond existence map, but the data sheet is not given. Can any one help me to solve this problem? With regards, Moutusi Manna Add whatever you love to the Yahoo! India homepage. Try now! http://in.rd.yahoo.com/tagline_metro_3/*http://in.yahoo.com/trynew ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] % of existence of hydrogen bond
Hi, The xpm-file matches the [ hbonds ] index group in the index file spat out by g_hbond. X:th line in the map is the h-bond given by the 4:th entry in the index group. Be careful when matching the rows though, because in the xpm file the first line of data is the bottom row of the matrix if I remember correctly. /Erik Moutusi Manna skrev: Dear all, I am dealing with a POPC+PEPTDE+WATER system. Basic residues of the peptide make hydrogen bonds with lipid headgroup (as reflected from g_rdf analysis) and the number of hydrogen bonds formed can be calculated from g_hbond program. Now, i want to calculate the % of trajectory time for which a bond between a particular group (say LYS and lipid headgroup po4) exist. -hbm gives a .xpm matrix, on solving (using xpm2ps) that i got a .eps file, which is a picture file of h_bond existence map, but the data sheet is not given. Can any one help me to solve this problem? With regards, Moutusi Manna Add whatever you love to the Yahoo! India homepage. Try now! http://in.rd.yahoo.com/tagline_metro_3/*http://in.yahoo.com/trynew ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- 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 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
