Hi, Thanks for your reply. I have written a script which gives the atoms with in certain cut-off distance from specified atom. I have added this to topology , the problem is that it creates topology from pdb but not the other way.
I use first pdb2gmx -f pdb -o gro -p top (command to generate gro,top). I use this topology file and add the bonds in this and use this topology for further use. Is this correct,?,but still i could not find bonds with other atoms when i load it in vmd. Please suggest me a way. Thanks, Mohan On Mon, Aug 27, 2012 at 10:29 PM, XAvier Periole <x.peri...@rug.nl> wrote: > > There is no script generating an elastic network in Gromacs. > > You could use the script that we developed in the context of the Martini CG > model (cgmartini.nl) but it would be certainly easier for you to simply > write a script that would rad the Clapha coordinates and define the ones > that are within a cut-off distance of your choice and then write a list of > bonds that you could add to a gromacs topology file ... > > > On Aug 26, 2012, at 3:34 PM, mohan maruthi sena wrote: > >> Hi all, >> I want to build elastic network model for a protein. To >> build an Elastic network model , I consider only C-alpha atoms of the >> protein. I want to make c-alpha atoms connect(make bond) with all the >> other c-alpha atoms , if it falls within certain cut-off distance. >> How can i do this? >> >> >> Please suggest me a way, >> >> Thanks, >> Mohan. >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Only plain text messages are allowed! >> * 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 > > > -- > 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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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