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'? 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
