Thanks Mark! This is exactly what I need.
---------------------------------------- > Date: Wed, 15 Aug 2012 22:18:10 +1000 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Parameters for bonded interactions > > On 15/08/2012 8:44 PM, Sebastien Cote wrote: > > After checking the post-processed topology, it does not contain the > > information that I need. I would like to know the torsion angle parameters > > of each torsion angle, and then compare with the ffbonded file to see the > > corresponding four-atom groups ' X X X X '. > > > > Is there a way to convert the .tpr file to 'human readable'? > > Sorry, meant to say that last email. gmxdump is all that is available. > You'll have to work backwards from the atom numbers (starting counting > from zero!) to get the interaction number to look up the interaction > parameters from their list. > > Mark > > > > > Thanks again, > > > > Sebastien > > > > ---------------------------------------- > >> Date: Wed, 15 Aug 2012 11:48:00 +1000 > >> From: mark.abra...@anu.edu.au > >> To: gmx-users@gromacs.org > >> Subject: Re: [gmx-users] Parameters for bonded interactions > >> > >> On 15/08/2012 9:46 AM, Sebastien Cote wrote: > >>> Dear Gromacs users, > >>> > >>> In the topology file of the protein, we see every two atoms that share a > >>> bond, three atoms that share a bond angle, and four atoms that share a > >>> torsion angle. However, the parameters (equilibrium value, energy > >>> constant, phase) are not explicitly shown as Gromacs fetch them in the > >>> ffbonded table. My question: Is there a simple way to see (without having > >>> to look at the code) which parameters are associated to which bond > >>> length, bond angle and torsion angle? > >>> > >>> More specifically, I would like to know which torsion angle parameters is > >>> specifically associated to each torsion angle. In the ffbonded table, > >>> there is sometimes different groups of four atoms that can be associated > >>> to the same torsion angle as there is the 'X' atom which can be any atom. > >> grompp -pp writes out a post-processed topology, which may be what you > >> need. > >> > >> Otherwise you can inspect the contents of the .tpr file to see which > >> interaction gets which parameters. That is not easy for a large system, > >> but is definitive. > >> > >> Mark > >> -- > >> 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 > > * 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 > * 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 * 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
