[gmx-users] g_ hbond on two peptides
Hi, I use g_hbond to analyze the system with two peptide. And I introduce the ndx file which include two group for the two peptides respectively. For the first prompt of g_hbond, I choose the group of the first peptide. For the second prompt, I choose the other peptide. I got the data that announced 4 H-bonds were found. And then I use rasmol to check, I found there are 2 intra-H-bonds in first peptide and 2 intra-H-bonds in the second. There are no inter-H-bonds between two peptides in my system. It's strange since I had selected different group to analyze when g_hbond promted. How should I do to exclude the intra-H-bond on one peptide? Hsin-Lin -- 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] g_ hbond on two peptides
Hsin-Lin Chiang skrev: Hi, I use g_hbond to analyze the system with two peptide. And I introduce the ndx file which include two group for the two peptides respectively. For the first prompt of g_hbond, I choose the group of the first peptide. For the second prompt, I choose the other peptide. I got the data that announced 4 H-bonds were found. And then I use rasmol to check, I found there are 2 intra-H-bonds in first peptide and 2 intra-H-bonds in the second. There are no inter-H-bonds between two peptides in my system. It's strange since I had selected different group to analyze when g_hbond promted. How should I do to exclude the intra-H-bond on one peptide? Hsin-Lin That sounds strange indeed. Have you looked into which hbonds are found? And are you sure your index file is error free? /Erik -- --- Erik Marklund, PhD student 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://folding.bmc.uu.se/ -- 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] g_ hbond on two peptides
On Jun 1, 2010, at 12:47 PM, Erik Marklund wrote: Hsin-Lin Chiang skrev: Hi, I use g_hbond to analyze the system with two peptide. And I introduce the ndx file which include two group for the two peptides respectively. For the first prompt of g_hbond, I choose the group of the first peptide. For the second prompt, I choose the other peptide. I got the data that announced 4 H-bonds were found. And then I use rasmol to check, I found there are 2 intra-H-bonds in first peptide and 2 intra-H-bonds in the second. There are no inter-H-bonds between two peptides in my system. It's strange since I had selected different group to analyze when g_hbond promted. How should I do to exclude the intra-H-bond on one peptide? Hsin-Lin That sounds strange indeed. Have you looked into which hbonds are found? And are you sure your index file is error free? You may also want to check that both programs define H-bond in the same manner. /Erik -- --- Erik Marklund, PhD student 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://folding.bmc.uu.se/ -- 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
