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Hello Eugene-- > I am trying to use the dna_refi.inp script to compute the structure of the > Dickerson dodecamer with some ribose sugar substitutions. Unfortunately the > structures, especially the base geometries are significantly distorted. > As you noted additional impropers have been added to the nucleic topology file. I believe that they are all to completely define methyl chirality, but that should be checked. One possibility is that these definitions are inconsistent with these experimental restraints. I will check further tomorrow. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkt0jVUACgkQPK2zrJwS/lapIACdEN95EyGtTHzs3c3oDuEF/Suv 6okAn2e3GbgeYzkqEXdhcBxdVWBEZxok =H56Y -----END PGP SIGNATURE-----
