TPRParser not detecting bonds.

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When loading with a .tpr as the topology bond information isn't taken from the 
tpr.

I've attached a simple system, just a box of flexible water.

The angles seem to be loaded fine, just not the bonds?  gmxdump tells me that 
the tpr has the bonds.

I've tried rolling back to the 0.8.1 release and bonds still aren't in _psf so 
I don't think we broke it recently with the class based topologies.

There's also not any testing for the topology loading in tpr files

Original issue reported on code.google.com by richardjgowers on 9 Mar 2015 at 11:17

Attachments:

• topol.tpr
• out.gro

[GoogleCodeExporter]

Original comment by richardjgowers on 9 Mar 2015 at 11:18

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There are plans to overhaul the TPR reader and I have some code by Tsjerk 
Wassenaar that will likely integrate nicely and it is complete and up-to-date 
(including 5.x I think) but I haven't had the time to play with it.

Unless the fix is quick, we could leave this open for 0.9.0 (just add a warning 
to document the problem) and then roll out a new TPR reader for 0.9.1 (under 
the hood it would be a big change but for the user it will just appear as a bug 
fix).

Oliver 

Original comment by orbeckst on 9 Mar 2015 at 5:29

[GoogleCodeExporter]

Hmm yeah.  There's a lot of cool information in .tprs, would be good to try and 
squeeze lots of this out into topology.

With the tpr being binary, it should be possible to make this very fast too.. 
which might be an alternate solution to Issue 212 for some people.

Original comment by richardjgowers on 19 Mar 2015 at 8:46