* PARAMETER_4. New parameter file for sugars developed by fitting to small * molecules and sugars. These parameters are meant to be compatible with the * Charmm23 force field, and were based upon Alex MacKerell's nucleic acid * parameters; wherever possible, his basic parameters, atom types, charges, * and van der Waals parameters have been retained. This set defines a * separate atom type CBS for the anomeric carbon C1 in beta sugar anomers. * Beta version; future revisions are still possible. * Guyan Liang and John Brady, Cornell University 09/08/95 * BONDS HOS OHS 546.4212 0.9595 HAS CTS 335.6034 1.1000 HAS CBS 335.6034 1.1052 CTS OHS 384.0792 1.4066 CBS OHS 384.0792 1.3932 CTS CTS 325.5297 1.5066 CBS CTS 325.5297 1.5074 CTS OES 385.3133 1.4165 CBS OES 385.3133 1.4202 HT OT 450.0 0.9572 ! from TIPS3P geometry HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) THETAS HAS CTS CTS 42.9062 109.7502 HAS CBS CTS 42.9062 109.7502 HAS CTS CBS 42.9062 109.7502 OHS CTS CTS 112.2085 107.6019 OHS CBS CTS 112.2085 107.6019 OHS CTS CBS 112.2085 107.6019 HOS OHS CTS 57.5478 109.1722 HOS OHS CBS 57.5478 109.1722 HAS CTS HAS 36.8220 106.1784 HAS CTS OHS 52.5070 109.3850 HAS CBS OHS 52.5070 109.3850 HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY HAS CTS OES 62.2500 106.4025 HAS CBS OES 62.2500 106.4025 CTS CTS CTS 167.3535 110.6156 CBS CTS CTS 167.3535 110.6156 CTS CTS OES 169.0276 108.3759 CBS CTS OES 169.0276 108.3759 CTS CBS OES 169.0276 108.3759 CTS OES CTS 92.5892 111.5092 CBS OES CTS 92.5892 111.5092 OES CTS OHS 74.2586 115.7322 OES CBS OHS 74.2586 110.3385 OES CTS OES 37.4370 112.1882 OES CBS OES 37.4370 106.9160 PHI CTS CTS CTS CTS -1.0683 1 0.0 CTS CTS CTS CTS -0.5605 2 0.0 CTS CTS CTS CTS 0.1955 3 0.0 CBS CTS CTS CTS -1.0683 1 0.0 CBS CTS CTS CTS -0.5605 2 0.0 CBS CTS CTS CTS 0.1955 3 0.0 CTS CTS CTS OES -1.2007 1 0.0 CTS CTS CTS OES -0.3145 2 0.0 CTS CTS CTS OES -0.0618 3 0.0 CBS CTS CTS OES -1.2007 1 0.0 CBS CTS CTS OES -0.3145 2 0.0 CBS CTS CTS OES -0.0618 3 0.0 CTS CTS CBS OES -1.2007 1 0.0 CTS CTS CBS OES -0.3145 2 0.0 CTS CTS CBS OES -0.0618 3 0.0 CTS CTS CTS OHS -1.9139 1 0.0 CTS CTS CTS OHS -0.3739 2 0.0 CTS CTS CTS OHS -0.0340 3 0.0 CTS CTS CBS OHS -1.9139 1 0.0 CTS CTS CBS OHS -0.3739 2 0.0 CTS CTS CBS OHS -0.0340 3 0.0 CBS CTS CTS OHS -1.9139 1 0.0 CBS CTS CTS OHS -0.3739 2 0.0 CBS CTS CTS OHS -0.0340 3 0.0 CTS OES CTS CTS -0.8477 1 0.0 CTS OES CTS CTS -0.3018 2 0.0 CTS OES CTS CTS 0.3763 3 0.0 CBS OES CTS CTS -0.8477 1 0.0 CBS OES CTS CTS -0.3018 2 0.0 CBS OES CTS CTS 0.3763 3 0.0 CTS OES CBS CTS -0.8477 1 0.0 CTS OES CBS CTS -0.3018 2 0.0 CTS OES CBS CTS 0.3763 3 0.0 HAS CTS CTS CTS 0.0000 1 0.0 HAS CTS CTS CTS 0.0000 2 0.0 HAS CTS CTS CTS 0.1441 3 0.0 HAS CBS CTS CTS 0.0000 1 0.0 HAS CBS CTS CTS 0.0000 2 0.0 HAS CBS CTS CTS 0.1441 3 0.0 HAS CTS CTS CBS 0.0000 1 0.0 HAS CTS CTS CBS 0.0000 2 0.0 HAS CTS CTS CBS 0.1441 3 0.0 HAS CTS CTS HAS 0.0000 1 0.0 HAS CTS CTS HAS 0.0000 2 0.0 HAS CTS CTS HAS 0.1595 3 0.0 HAS CBS CTS HAS 0.0000 1 0.0 HAS CBS CTS HAS 0.0000 2 0.0 HAS CBS CTS HAS 0.1595 3 0.0 HAS CTS OES CTS 0.0000 1 0.0 HAS CTS OES CTS 0.0000 2 0.0 HAS CTS OES CTS 0.2840 3 0.0 HAS CBS OES CTS 0.0000 1 0.0 HAS CBS OES CTS 0.0000 2 0.0 HAS CBS OES CTS 0.2840 3 0.0 HAS CTS OES CBS 0.0000 1 0.0 HAS CTS OES CBS 0.0000 2 0.0 HAS CTS OES CBS 0.2840 3 0.0 HOS OHS CTS CTS 1.0504 1 0.0 HOS OHS CTS CTS 0.1336 2 0.0 HOS OHS CTS CTS 0.3274 3 0.0 HOS OHS CBS CTS 1.0504 1 0.0 HOS OHS CBS CTS 0.1336 2 0.0 HOS OHS CBS CTS 0.3274 3 0.0 HOS OHS CTS CBS 1.0504 1 0.0 HOS OHS CTS CBS 0.1336 2 0.0 HOS OHS CTS CBS 0.3274 3 0.0 HOS OHS CTS HAS 0.0000 1 0.0 HOS OHS CTS HAS 0.0000 2 0.0 HOS OHS CTS HAS 0.1694 3 0.0 HOS OHS CBS HAS 0.0000 1 0.0 HOS OHS CBS HAS 0.0000 2 0.0 HOS OHS CBS HAS 0.1694 3 0.0 OES CTS CTS HAS 0.0000 1 0.0 OES CTS CTS HAS 0.0000 2 0.0 OES CTS CTS HAS 0.1686 3 0.0 OES CBS CTS HAS 0.0000 1 0.0 OES CBS CTS HAS 0.0000 2 0.0 OES CBS CTS HAS 0.1686 3 0.0 OES CTS CBS HAS 0.0000 1 0.0 OES CTS CBS HAS 0.0000 2 0.0 OES CTS CBS HAS 0.1686 3 0.0 OES CTS CTS OES -2.6785 1 0.0 OES CTS CTS OES 0.7851 2 0.0 OES CTS CTS OES 0.2552 3 0.0 OES CBS CTS OES -2.6785 1 0.0 OES CBS CTS OES 0.7851 2 0.0 OES CBS CTS OES 0.2552 3 0.0 OES CTS CTS OHS -3.7993 1 0.0 OES CTS CTS OHS 0.5688 2 0.0 OES CTS CTS OHS 0.4204 3 0.0 OES CBS CTS OHS -3.7993 1 0.0 OES CBS CTS OHS 0.5688 2 0.0 OES CBS CTS OHS 0.4204 3 0.0 OES CTS CBS OHS -3.7993 1 0.0 OES CTS CBS OHS 0.5688 2 0.0 OES CTS CBS OHS 0.4204 3 0.0 OES CTS OES CTS 0.1948 1 0.0 OES CTS OES CTS 0.9778 2 0.0 OES CTS OES CTS 0.9115 3 0.0 OES CBS OES CTS 0.1948 1 0.0 OES CBS OES CTS 0.9778 2 0.0 OES CBS OES CTS 0.9115 3 0.0 OHS CTS OES CTS 1.9193 1 0.0 OHS CTS OES CTS 1.0102 2 0.0 OHS CTS OES CTS 0.7294 3 0.0 OHS CBS OES CTS 1.9193 1 0.0 OHS CBS OES CTS 1.0102 2 0.0 OHS CBS OES CTS 0.7294 3 0.0 OES CTS OHS HOS 1.2936 1 0.0 OES CTS OHS HOS 1.3295 2 0.0 OES CTS OHS HOS 0.4323 3 0.0 OES CBS OHS HOS 1.2936 1 0.0 OES CBS OHS HOS 1.3295 2 0.0 OES CBS OHS HOS 0.4323 3 0.0 OHS CTS CTS HAS 0.0000 1 0.0 OHS CTS CTS HAS 0.0000 2 0.0 OHS CTS CTS HAS 0.1472 3 0.0 OHS CBS CTS HAS 0.0000 1 0.0 OHS CBS CTS HAS 0.0000 2 0.0 OHS CBS CTS HAS 0.1472 3 0.0 OHS CTS CBS HAS 0.0000 1 0.0 OHS CTS CBS HAS 0.0000 2 0.0 OHS CTS CBS HAS 0.1472 3 0.0 OHS CTS CTS OHS -4.9362 1 0.0 OHS CTS CTS OHS 0.2907 2 0.0 OHS CTS CTS OHS 0.4638 3 0.0 OHS CBS CTS OHS -4.9362 1 0.0 OHS CBS CTS OHS 0.2907 2 0.0 OHS CBS CTS OHS 0.4638 3 0.0 NONBONDED NBXMOD 5 atom CDIEL shift vatom VDISTANCE VSWITCH - CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5 ! ! Emin Rmin ! (kcal/mol) (A) HOS 0.00 -0.0460 0.2245 ! from alex's para_na, hn5 HAS 0.00 -0.0220 1.3200 ! from alex's para_na, hn6 ! CTS 0.00 -0.0200 2.2750 0.000 -0.01000 1.90000 ! from alex's para_na, cn6 CBS 0.00 -0.0200 2.2750 0.000 -0.01000 1.90000 ! from alex's para_na, cn6 OHS 0.00 -0.1521 1.7700 ! from para_na, on5 ! OES 0.00 -0.1521 1.7700 ! from para_na, on6 ! HT 0.00 -0.046 0.2245 !TIP3P water hydrogen, from Alex' para_na ! OT 0.00 -0.1521 1.7682 !TIP3P water oxygen, from Alex' para_na ! NBFIX ! HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use ! READ PARAM APPEND CARD ! to append hbond parameters from the file: par_hbond.inp END