RE: [gmx-users] Parameters for bonded interactions
Thanks a lot Mark! 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 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
RE: [gmx-users] Parameters for bonded interactions
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 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
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 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 * 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
RE: [gmx-users] Parameters for bonded interactions
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 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
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 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
