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
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