********> bugfix.21 Author: Piotr Cieplak Date: 6/12/95 Problem: wrong placement of H3' atoms of ribonucleic acids in '94 force field Severity: moderate Affects: default positioning of H3' when none are supplied by an input PDB file Fix: (All internal torsion angles for placing H3' are set to the same value in all RNA and DNA residues, whether or not there was a problem. The critical ones are the ones that are -80.) Make the changes below to all_nuc94.in, then: % pwd [path]/amber41/dat % make db94.dat % cd ../leap/lib % rm all*94.lib ff94.log % tLeap !not 'tleap' - note capital 'L' > source ff94.cmd !ignore errors & warnings if tLeap > q % cp all_nucleic94.lib [leap_install_path]/Leap/lib/ ------------------------------------------------------------------------- 285c285 < 29 H3' H1 E 28 9 6 1.09 109.50 -80.00 0.0615 --- > 29 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0615 349c349 < 31 H3' H1 E 30 11 8 1.09 109.50 -80.00 0.0615 --- > 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0615 413c413 < 31 H3' H1 E 30 11 8 1.09 109.50 -80.00 0.0615 --- > 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0615 476c476 < 29 H3' H1 E 28 9 6 1.09 109.50 -80.00 0.0615 --- > 29 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0615 785c785 < 26 H3' H1 E 25 9 6 1.09 109.50 -80.00 0.0615 --- > 26 H3' H1 E 25 9 6 1.09 109.50 30.00 0.0615 845c845 < 28 H3' H1 E 27 11 8 1.09 109.50 -80.00 0.0615 --- > 28 H3' H1 E 27 11 8 1.09 109.50 30.00 0.0615 905c905 < 28 H3' H1 E 27 11 8 1.09 109.50 -80.00 0.0615 --- > 28 H3' H1 E 27 11 8 1.09 109.50 30.00 0.0615 965c965 < 26 H3' H1 E 25 9 6 1.09 109.50 -80.00 0.0615 --- > 26 H3' H1 E 25 9 6 1.09 109.50 30.00 0.0615 1028c1028 < 30 H3' H1 E 29 9 6 1.09 109.50 -320.00 0.0985 --- > 30 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0985 1084c1084 < 32 H3' H1 E 31 11 8 1.09 109.50 -320.00 0.0985 --- > 32 H3' H1 E 31 11 8 1.09 109.50 30.00 0.0985 1140c1140 < 32 H3' H1 E 31 11 8 1.09 109.50 -320.00 0.0985 --- > 32 H3' H1 E 31 11 8 1.09 109.50 30.00 0.0985 1195c1195 < 30 H3' H1 E 29 9 6 1.09 109.50 -320.00 0.0985 --- > 30 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0985 1259c1259 < 30 H3' H1 E 29 9 6 1.09 109.50 -80.00 0.0615 --- > 30 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0615 1325c1325 < 32 H3' H1 E 31 11 8 1.09 109.50 -80.00 0.0615 --- > 32 H3' H1 E 31 11 8 1.09 109.50 30.00 0.0615 1391c1391 < 32 H3' H1 E 31 11 8 1.09 109.50 -80.00 0.0615 --- > 32 H3' H1 E 31 11 8 1.09 109.50 30.00 0.0615 1456c1456 < 30 H3' H1 E 29 9 6 1.09 109.50 -80.00 0.0615 --- > 30 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0615 1518c1518 < 27 H3' H1 E 26 9 6 1.09 109.50 -320.00 0.0985 --- > 27 H3' H1 E 26 9 6 1.09 109.50 30.00 0.0985 1578c1578 < 29 H3' H1 E 28 11 8 1.09 109.50 -320.00 0.0985 --- > 29 H3' H1 E 28 11 8 1.09 109.50 30.00 0.0985 1638c1638 < 29 H3' H1 E 28 11 8 1.09 109.50 -320.00 0.0985 --- > 29 H3' H1 E 28 11 8 1.09 109.50 30.00 0.0985 1698c1698 < 27 H3' H1 E 26 9 6 1.09 109.50 -320.00 0.0985 --- > 27 H3' H1 E 26 9 6 1.09 109.50 30.00 0.0985 1757c1757 < 27 H3' H1 E 26 9 6 1.09 109.50 -80.00 0.0615 --- > 27 H3' H1 E 26 9 6 1.09 109.50 30.00 0.0615 1818c1818 < 29 H3' H1 E 28 11 8 1.09 109.50 -80.00 0.0615 --- > 29 H3' H1 E 28 11 8 1.09 109.50 30.00 0.0615 1880c1880 < 29 H3' H1 E 28 11 8 1.09 109.50 -80.00 0.0615 --- > 29 H3' H1 E 28 11 8 1.09 109.50 30.00 0.0615 1941c1941 < 27 H3' H1 E 26 9 6 1.09 109.50 -80.00 0.0615 --- > 27 H3' H1 E 26 9 6 1.09 109.50 30.00 0.0615 ------------------------------------------------------------------------- Temporary workarounds: provide a PDB file with proper placement, e.g. adjusted by hand.