Hi Charles, This clears up the problem with the geometric energy terms in the refine_full.inp calculation. The resulting energies are:
REMARK FILENAME="test_full_nocoup_1.sa" REMARK =============================================================== REMARK overall,bonds,angles,improper,vdw,noe,cdih,dipo,rama,ncs,orie,plan,coup,dcsa REMARK energies: 7463.83, 56.7333, 624.665, 23.0412, 76.5582, 107.253, 0, 8008.66, -1346.55, 306.293, -944.449, 17.5586,103.479, compared to the following energies generated using the psf file generated with nucleic.top/par: REMARK FILENAME="test_full_nocoup_1.sa" REMARK =============================================================== REMARK overall,bonds,angles,improper,vdw,noe,cdih,dipo,rama,ncs,orie,plan,coup,dcsa REMARK energies: 37050.2, 2329.45, 9680.19, 15715.1, 915.524, 822.767, 0.241548, 7967.06, -1315.5, 1283.43, -777.791, 4.82553,, However, although the geometric energy terms are also much lower in the refine_full.py calculation, i.e., REMARK ------------------------------------------------------------ REMARK summary Name Energy RMS Violations REMARK summary total 3987.60 877 REMARK summary ANGL 924.26 2.028 328 REMARK summary BOND 215.03 0.016 19 REMARK summary CDIH 22.36 1.668 4 REMARK summary IMPR 41.09 0.717 8 REMARK summary NCS 280.46 REMARK summary ORIE -598.45 REMARK summary PLAN 39.36 , compared to the nucleic.top/par calculation, i.e., REMARK ------------------------------------------------------------ REMARK summary Name Energy RMS Violations REMARK summary total 77782.66 785 REMARK summary ANGL 934.87 2.039 295 REMARK summary BOND 252.82 0.018 23 REMARK summary CDIH 21.94 1.652 2 REMARK summary IMPR 76386.18 28.835 46 REMARK summary NCS 651.75 REMARK summary ORIE -854.54 REMARK summary PLAN 7.04 , The number of experimental violations is still quite large, and the G24-C1 and G12-C13 base interactions are still distorted. Eugene Eugene DeRose, Ph.D. NIEHS NMR Laboratory Manager Global Health Sector SRA International, Inc. Contractor to NIEHS/DIR National Institute of Environmental Health Sciences Research Triangle Park, NC 27709 919.541.1981 voice 919.541.5707 fax derose at niehs.nih.gov www.niehs.nih.gov www.sra.com Enhancing Human Health Around the World Everyday -- On 2/12/10 4:32 PM, "Charles at Schwieters.org" <Charles at Schwieters.org> wrote: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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/><http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkt1yNAACgkQPK2zrJwS/laQsQCfZu6NBHVoLXIPfZr5VEB8hrHY UuQAn0G+J5GwGuHp3UkyDmjSo99qg8E2 =v6nX -----END PGP SIGNATURE-----
