Re: [gmx-users] Elastic network model -building
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 listgmx-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 listgmx-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
Re: [gmx-users] Elastic network model -building
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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Elastic network model -building
On Aug 27, 2012, at 7:14 PM, mohan maruthi sena wrote: 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. Not clear what the other way around is! 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,? I have no idea! It depends what you want to do! Doing like you describe you add a elastic network to a atomistic description ... if this is not the objective do something that would follow your idea! ,but still i could not find bonds with other atoms when i load it in vmd. Please suggest me a way. VMD defines default bonds according to their distances in the structure you give. So between Calpha the distance is about 0.38 nm ... if you use a dynamic bond description in VMD and select the Calphas ... a cutoff of 4.0 would show you the connections. 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 listgmx-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 listgmx-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 listgmx-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 -- gmx-users mailing listgmx-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
[gmx-users] Elastic network model -building
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 listgmx-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
