Hi all,
I need a pdb file of an RNA triplex to do Molecular Dynamics Simulations. Do you know what software or method can be used to create structures of a (the) standard RNA triplex? Thanks a lot.
Hi,
If you want a "pdb" file from any other file format than you can use Open Babel software.
Danish J
There should be some DNA/RNA structure generator available in more than one software package. Included is a link for a DNA/RNA tutorial that includes (now) free software. If you know the sequence you should be able to construct it and save it as a PDB file.
Included is also a link to a PDB entry for RNA triplex, though I would suspect you want a specific sequence? If it is available you can just download it.
In any case, after constructing the sequence, "forcing" the structure using restraints/constraints should be possible. Though I'm not sure if it would require modification of "standard RNA forcefield" for simulation.
http://ambermd.org/tutorials/advanced/tutorial4/
http://www.rcsb.org/pdb/explore.do?structureId=437D
To Danish Jasnaik ,
Thank you, Danish. Yes, the Open Babel software is powerful and useful in creating chemical data file. However, my problem is that I have nothing information about triplex except their sequences. So, I hope there are some tools, which can be used to produce RNA triplex from a sequence. Thank you all the same.
To Gustaf D Olsson,
Thank you very much for your answer. As you said, there are some DNA/RNA structure generators available in more than one software package, such as NAB tool in Amber package. However, these tools can usually be used to generate dsRNA/dsDNA , and it is still difficult for them to produce a RNA/DNA triplex from sequences.
Thanks again.
Hi,
OSDD (Open Source Drug Discovery database will provide you with good options, while you can also try this server;
http://iimcb.genesilico.pl/modernaserver/
Hope this helps
Regards
Hi,
MMB (MacroMoleculeBuilder) is best choice in your case. MMB needs just sequence of your RNA or DNA then gives a .pdb file as output.
Https://simtk.org/home/rnatoolbox
After creating your molecule you have to minimize it by your simulation software to obtain a good initial structure for simulation.
To Amir Abbasi,
Hi, Amir, thank you for your answer. Yes, MMB (also known as RNAbuilder) is powerful in RNA 3D structure prediction. However, as a homology-based method, I wonder if it can be used to predict RNA triplex, because the known information of triplex in PDB is still limited. Even so, I will try. Thank you very much.
To Danish,
OSDD is a new tool for me. I will try to use it. I hope it can work well in my issue. Thanks very much.
Best regards.
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