Hi Yaqi, You will need to change a few things to follow the POPS conventions: 1. the single-letter residue name should be in column 20, whereas RNABuilder has that in column 18. Just move the whole column over by two spaces without changing any of the other columns. This can be done with a global search-replace, or in some other way depending on your text editor. 2. You should use single-quotes rather than asterisks in atom names. For example, C1' is ok, C1* is not. This can be fixed with a global search-replace. 3. A different error occurs if any atoms are too close together. This can be fixed probably by using setting "addAllHeavyAtomSterics TRUE" and running for a short time. This will put steric spheres on all atoms except hydrogen. It's expensive, but you may only need to run for a short time. The RNABuilder input file conventions have changed. You should take a look at the RNABuilder 2.0 tutorial, which is available on the Downloads page. If you have any trouble you can send me the new contacts.dat file and I can help you update it so it runs with RNABuilder 2.0. Sam On Aug 19, 2010, at 11:56 PM, Yaqi Wan wrote:

Hi Sam,

How is going! I am finally working on the manuscript of Bangia group I ribozyme now and have all ready got most of the pieces. I hope I can send it to you guys first and then to Biochemistry by October. So I will start to bother you again and ask you questions about RNABuilder~. The first thing I am going to do is try your new RNABuilder and see if it can improve my model, since some part of it does not have perfect helices. The other thing I want to try is to generate solvent accessibility data from the Bangia ribozyme model and compare this ideal data with my experimental one. But I met some problems with that, the web server doesn't recognize the .pdb file of my model. I guess it is because the residue/atom naming is different in RNABuilder and the pdb format? Do you know how to match them or change the output of RNABuilder? The web server is http://mathbio.nimr.mrc.ac.uk/wiki/POPS And the paper introducing it is http://www.ncbi.nlm.nih.gov/pubmed/12824328

Thanks a lot~!! Yaqi

-----Original Message----- From: Samuel Coulbourn Flores [mailto:samuelfloresc@gmail.com] Sent: Monday, July 26, 2010 4:03 PM To: Erich Chapman; Boris Fuertig; jennifer.boots@univie.ac.at; Bob Zimmermann; thomas.gstrein@univie.ac.at; andreas.liebeg@univie.ac.at; nora.sachsenmaier@univie.ac.at; georgeta.zemora@univie.ac.at; Christina Waldisch; Francois Major; p.dallaire@sympatico.ca; p.jifroodian-haghighi@umontreal.ca; marc.frederic.blanchet@umontreal.ca; nicolas.scott@umontreal.ca; David Mitchell; frederique.badeaux@umontreal.ca; Rick Russell; Yaqi Wan; isabelle.filiatreault@umontreal.ca Subject: New RNABuilder 2.0 executables

Hi Guys,

I just finished an RNABuilder 2.0 binary distribution for Windows, Snow Leopard, Leopard, and CentOS. There is also an accompanying tutorial. The 2.0 release contains lots of new features including control blocks, springs between atoms and from atoms to ground, potential rescaling / simulated annealing support, and much more. In particular, the base-wise force field now enforces the distance between corresponding C1' atoms for much improved speed and fidelity.

Please download from here if interested:

https://simtk.org/project/xml/downloads.xml?group_id=359

Let me know if I can be of help with your projects.

Sam