[gmx-users] Extracting bond information from topol.tpr file using template.c

Mark Abraham Mark.Abraham at anu.edu.au
Wed Sep 19 05:49:22 CEST 2012

On 19/09/2012 12:49 PM, Amit Shavit wrote:
> Hello,
> I'm relatively new to GROMACS, and I need to write some of my own analysis
> tools using the template.c file.
> I have been able to figure out most of the structure of it, and how the C
> Structs are used. That is to say, I can successfully retrieve particle
> positions, residue IDs, residue names, etc.
> The one piece of information that I can't seem to be able to retrieve is
> bonding information. Is there a way for me to get this? I should mention
> that I run the program by inputting a traj.trr and topol.tpr files, so I
> have access to the information saved in those files.

The easiest way to learn how to use the information in the .tpr is to 
work by analogy from an existing tool that has to parse the bonding 
information, preferably in a similar way. I just can't think of one that 
really looks at the bonding topology, rather than using a set of atoms 
belonging to a group, residue or molecule.

Why do you want the bonding information? Maybe you don't need it...


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