[RNABuilder-help] Re: Compiling RNABuilder

[Samuel Flores]

Hi Kristian,

This error message is telling you that you need to set removeRigidBodyMomentum to false:

removeRigidBodyMomentum False

.. sometime before you issue the constraint command.  

The error message is perhaps a bit deceptive.  You did not explicitly set removeRigidBodyMomentum True, that is simply the default and the error message does not discriminate between those two cases.


I don't recommend compiling from source, it's a bit tedious and usually I do it when the user and I are in the same room or logged into the same computer.  I just put up RNABuilder 2.1 binaries for Linux a minute ago, and could do the same for Snow Leopard, if you are using those operating systems.  Windows will probably have to wait until January when I go back to visit Stanford.


What are you using RNABuilder for, if it's not confidential?  I will be happy to provide advice.  Also, I'm now based in Europe and would be happy to think about setting up a workshop if you know a few people that would participate.

Sam  




On Nov 3, 2010, at 11:58 AM, Kristian Rother wrote:

> You have been contacted by a member of Simtk.org.
> 
> From: Kristian Rother
> Email: krother at rubor.de
> 
> The e-mail was sent via the "contact" link on Simtk.org by the above member. It is not screened by Simtk.org or its staff.
> 
> 
> *** MESSAGE BEGINS ***
> 
> 
> Dear Sam,
> 
> I'm having trouble using the Weld constraint in RNABuilder. It says:
> SimTK Exception thrown at Repel.cpp:286:
> Error detected by SimTK method [Repel.cpp]: At this time it is not possible to apply a constraint AND turn on removeRigidBodyMomentum.  Please remove one of the two.
> 
> - in the input script, there is nothing else than the starting structure, the reporting interval, and the Weld constraint set.
> 
> Then, I tried to upgrade RNABuilder by compiling the code from SVN with SimTK Version: 2.1.0. I get a compilation error: 
> 
> In file included from /usr/local/SimTK/include/SimTKcommon/basics.h:52,
>                from /usr/local/SimTK/include/SimTKcommon.h:40,
>                from /usr/local/SimTK/include/SimTKsimbody.h:70,
>                from /usr/local/SimTK/include/SimTKmolmodel.h:86,
>                from /home/krother/rnabuilder/repo/rnatoolbox/trunk/include/Repel.h:38,
>                from Repel.cpp:31:
> /usr/local/SimTK/include/SimTKcommon/internal/String.h:296: error: explicit template specialization cannot have a storage class
> /usr/local/SimTK/include/SimTKcommon/internal/String.h:301: error: explicit template specialization cannot have a storage class
> 
> This might be related to versions - do you have any recommendation?
> 
> Best Regards,
>  Kristian
> 
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