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Hello again 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. > I think the issue is indeed a topology file mismatch. In refine_full.inp, please replace nucleic.top/par with nucleic-1.0.top/par, and do this to refine_full.py: add these lines: protocol.topology['nucleic'] = "nucleic-1.0.top" protocol.parameters['nucleic'] = "nucleic-1.0.par" before the protocol.initParams line. I previously made this change to ensemble.py, but forgot to update the other files. The starting structure is not consistent with the current topology/parameters. Please let me know if this clears things up. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkt1yNAACgkQPK2zrJwS/laQsQCfZu6NBHVoLXIPfZr5VEB8hrHY UuQAn0G+J5GwGuHp3UkyDmjSo99qg8E2 =v6nX -----END PGP SIGNATURE-----
