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 have noticed that the sample refine_full.inp script generates a good structure for the sample DNA calculation in eginput/dna_refi as long as the psf file provided, dna_new.psf, is used, i.e., 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: 7430.46, 56.3133, 593.507, 10.1168, 76.1481, 114.733, 0, 8004.42, -1340.35, 306.109, -946.373, 17.2073,106.849, However, if a new structure file is generated using eginput/dna/dna.inp the geometric energy terms increase dramatically and the base geometry is significantly distorted, i.e., 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, The use of this psf file in the sample eginput/dna/full_ring_03.inp calculation also results in high energies: REMARK FILENAME="full_ring_03_1.sa" REMARK =============================================================== REMARK overall,bonds,angles,improper,vdw,noe,cdih,xdip,rama,ncs,orie,plan REMARK energies: 31243, 2993.69, 9027.05, 18832.2, 398.815, 653.736, 5.06793, 1587.24, -3273.41, 1713.71, -704.531, 9.39292 Upon comparison of the dna_new.psf file provided and the newly created psf file, I noticed that the new file has more improper terms defined. As a side note, the sample refine_full.py calculation also produces high energies with a significant number of experimental violations: 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 REMARK summary RAMA -1267.03 REMARK summary VDW 57.52 2 REMARK summary csa 43.94 2.235 44 REMARK summary jcoup 5.63 0.160 22 REMARK summary noe 53.87 0.053 0 REMARK summary rdcs 1488.67 0.537 351 Any suggestions on what might be causing the problem with the psf files will be greatly appreciated. Thanks, 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 --
