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Hello Usman-- > > I am using Xplor-NIH for structure determination of nucleic acids. I > have used anneal scripts and refinement scripts to produce two > separate RNA structures. What I would like to do is to use Xplor to > model RNA-RNA interactions between these two RNA structures. > > But before I ask you how to produce a script to incorporate RNA-RNA > interactions, I would like to know how to generate water or produce a > water box to surround an RNA structure. I have also read in the manual > that you can further refine your structure using a water refinement > protocol. Will this protocol generate water molecules around an RNA > structure and then start the refinement step. > While others have employed explicit solvent, I have not- so you will have to get this sort of script from others. Instead, we employ database potentials for torsion angles and nucleotide positional information. An example of using these terms can be found in eginput/rna_refi in the Xplor-NIH distribution. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkpvDPcACgkQPK2zrJwS/lYCCQCfSKz4AA7jkL9SS63nj7fGmChQ WocAn1THNszC78UVYY+h9GVgTiLjfJaw =DoO7 -----END PGP SIGNATURE-----
