Hi, First of all, thank you for your attention. I used g_hbond in order to analyze hydrogen bonds formed;but, I need a more detailed information. The command that you mentioned is capable of giving information about hydrogen bonds formed in each frame. However, I want to investigate the exact donor and acceptor groups in each frame. In this respect, I converted the xtc file to a pdb file to get all of the coordinates of both water and protein molecules. What should I do?
Thanks in advance Ozge -----Original Message----- From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Wed, 28 Feb 2007 17:52:34 +0100 Subject: Re: [gmx-users] problem with trjconv Hi Ozge, Why do you first want to go to a .pdb trajectory? Gromacs comes with g_hbond, which can analyze hydrogen bonds for you, as well as giving you an index file containing the atoms involved in hydrogen bonds, which you can use to extract those from your trajectory. In addition, g_hbond also does "normal" contacts, other than hydrogen bonds. Tsjerk On 2/28/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > OZGE ENGIN wrote: > > Hi, > > > > I have a problem with the trjconv command. > > > > I performed a 30 ns simulation, and wanted to analyze hydrogen bonds formed > > between protein and water molecules. In this respect, I converted the xtc > > file into a pdb file by selecting system option. As you can understand the > > overall file was such a large file that I could not handle it. So, I want > > to know whether there is any possibility to select water molecules within a > > cutoff value or to extract frames within given time steps? For instance, > > at every 70 th step, from 70 ps to 80 ps. > > If you read the man page for trjconv, you will see an option to do the > latter. I don't think the former is implemented in the gromacs utilities. > > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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 _______________________________________________ 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
