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

Erik Marklund erikm at xray.bmc.uu.se
Wed Sep 19 09:30:25 CEST 2012

g_hbond does.

19 sep 2012 kl. 05.49 skrev Mark Abraham:

> 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...
> Mark
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Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se

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