REMARKS Parameter file for NAG REMARKS ================================== REMARKS John Vakonakis 08/05/2007 REMARKS Adapted from PARAM3.CHO. To be used with PROTEIN.PAR REMARKS Parameters from the 1.5A crystal structure (1LZB.PDB) set echo=false end evaluate ($kbon = 1000) ! kcal / mol-A^2 evaluate ($kang = 500) ! kcal / mol-rad^2 evaluate ($kchi = 500) ! kcal / mol-rad^2 evaluate ($kback = 500) evaluate ($kpx = $kback) if ( $exist_weak_omega = TRUE ) then if ( $weak_omega=1 ) then evaluate ($kpx = $kback*0.5) display reducing the omega improper force constant end if end if evaluate ($kpla = 500) ! kcal / mol-rad^2 {Lengths from the crystal structure} bond CC OE $kbon 1.440 bond CCE OE $kbon 1.399 bond CC CC $kbon 1.516 bond CC CC6 $kbon 1.528 bond CCE CC $kbon 1.506 bond CC HA $kbon 1.080 bond CC6 HA $kbon 1.080 bond CCE HA $kbon 1.080 bond CC OH $kbon 1.435 bond CC6 OH $kbon 1.437 bond CCE OH $kbon 1.395 bond CC NH1 $kbon 1.470 bond CCE NH1 $kbon 1.450 bond CC C $kbon 1.509 {Angles unchanged from param3.cho} angle H OH CC $kang 109.35 angle H OH CC6 $kang 109.35 angle H OH CCE $kang 109.35 angle HA CC HA $kang 107.85 angle HA CC6 HA $kang 107.85 angle HA CC CC $kang 108.72 angle HA CC6 CC $kang 108.72 angle HA CC CC6 $kang 108.72 angle HA CC CCE $kang 108.72 angle HA CCE CC $kang 108.72 angle HA CC OH $kang 109.89 angle HA CC6 OH $kang 109.89 angle HA CCE OH $kang 109.89 angle HA CC OE $kang 107.24 angle HA CCE OE $kang 109.24 !2007/12/04 CDS tweaked for consistency angle CC CC CC $kang 110.40 angle CC CC CC6 $kang 112.50 angle CCE CC CC $kang 110.40 angle CC CC6 OH $kang 111.20 angle CC CCE OH $kang 109.70 angle CCE CC OH $kang 109.70 angle CC CC OH $kang 109.70 angle CC CC OE $kang 110.00 angle CC6 CC OE $kang 107.20 angle CC CCE OE $kang 110.00 angle CC OE CCE $kang 112.0 angle OE CCE OH $kang 108.0 angle O C CC $kang 120.0 angle C CC HA $kang 109.5 angle CC CC NH1 $kang 110.0 angle CCE CC NH1 $kang 110.0 angle HA CC NH1 $kang 109.5 angle CC NH1 H $kang 120.0 angle CC NH1 C $kang 120.0 angle NH1 CC OE $kang 110.7 angle NH1 C CC $kang 117.5 angle CCE NH1 C $kang 120.0 angle CCE NH1 H $kang 120.0 angle CC CCE NH1 $kang 110.0 angle NH1 CCE OE $kang 110.7 angle HA CCE NH1 $kang 109.5 {idealized, observed values from the crystal structure as comment} IMPRoper OH CCE CC CC $kpla 0 180 !175.069 IMPRoper OE CCE CC NH1 $kpla 0 180 !173.816 IMPRoper OH CCE OE CC $kpla 0 180 !-178.137 IMPRoper CCE CC CC OH $kpla 0 180 !-171.955 IMPRoper CC6 CC OE CCE $kpla 0 180 !174.889 IMPRoper CC C NH1 CC $kpx 0 180 !179.660 IMPRoper O C NH1 CC $kpx 0 0 !-1.111 IMPRoper CCE CC OH OE $kchi 0 35 !34.218 IMPRoper CC NH1 CC CCE $kchi 0 35 !35.152 IMPRoper CC CC CC OH $kchi 0 35 !34.689 IMPRoper CC OH CC CC $kchi 0 35 !32.587 IMPRoper CC OE CC6 CC $kchi 0 35 !33.858 IMPRoper C CC NH1 O $kchi 0 0 !0.388 IMPRoper C NH1 CCE HA $kpx 0 0 IMPRoper CT C NH1 CCE $kpx 0 180 IMPRoper NH1 C CCE H $kpx 0 0 improper HA HA C HA $kchi 0 -66.514 ! methyl improper HA HA CC OH $kchi 0 -70.44 ! IMPRoper NH1 CCE CC CC $kpla 0 180 IMPRoper NH1 CCE OE CC $kpla 0 180 IMPRoper CCE CC NH1 OE $kchi 0 35 NONBonded CC6 0.0903 3.2072 0.0903 3.2072 NONBonded CCE 0.0903 3.2072 0.0903 3.2072 NONBonded OE 0.1591 2.8509 0.1591 2.8509 set echo=true end