Hello Sir, I used C-alpha atoms.
Kavya On Mon, Feb 18, 2013 at 11:28 PM, Erik Marklund <[email protected]>wrote: > Hi, > > With -r2 one can provide a second, larger, cutoff so that contact kinetics > can be analyzed within the Luzar-Chandler framework that were designed for > hbonds. > > What index groups did you use? > > Erik > > > On Feb 18, 2013, at 6:04 PM, Kavyashree M wrote: > > Dear users, >> >> As Suggested by Erik, I used g_hbond with -contact to obtain a matrix of >> each contact as a function of time. I used the following command - >> g_hbond -f a.xtc -s a.tpr -contact -r2 0.5 -hbm m.xpm -b 4000 -e 4400 -hbn >> c.ndx >> >> I get only three contacts in the index file. The protein is a dimer of 474 >> residues >> (237 each). With a distance cut off of 0.5nm there should have been more >> number >> of contacts. And what is the difference in using -r only or -r2 only and >> combining -r >> and -r2? >> >> Thank you >> Kavya >> >> On Thu, Feb 14, 2013 at 3:40 PM, Kavyashree M <[email protected]> wrote: >> >> Thank you! >>> >>> >>> On Thu, Feb 14, 2013 at 3:38 PM, Erik Marklund <[email protected] >>> >wrote: >>> >>> Perhaps g_hbond -contact will do what you want. >>>> >>>> Erik >>>> >>>> >>>> On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote: >>>> >>>> Dear users, >>>> >>>>> >>>>> How can I get the number of interactions of each residue >>>>> within a cut off as a function of time. just like g_saltbr writes >>>>> with the option -sep. >>>>> I tried using g_mdmat but it gives an average contact map. >>>>> >>>>> Thank you >>>>> Kavya >>>>> -- gmx-users mailing list [email protected] >>>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>> > >>>>> * Please search the archive at http://www.gromacs.org/** >>>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>>>> Mailing_Lists/Search<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 [email protected]. >>>>> * Can't post? Read >>>>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>>> > >>>>> >>>>> >>>> -- >>>> gmx-users mailing list [email protected] >>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> > >>>> * Please search the archive at http://www.gromacs.org/** >>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>>> posting! >>>> >>>> * Please don't post (un)subscribe requests to the list. Use thewww >>>> interface or send it to [email protected]. >>>> * Can't post? Read >>>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>> > >>>> >>>> >>> >>> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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 [email protected]. >> * Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
