remarks file toppar/carbohydrate.param REMARKS Parameter file for pyranose sugars for crystallographic remarks structure determination. remarks REMARKS Bill Weis 10-July-1988 REMARKS Additions for atom type combinations not covered in PARAM19X.PRO. REMARKS Needed additions are for ether oxygen and aliphatic carbon in all-atom REMARKS representation used for sugars (type CC). Ditto for type HA. REMARKS Values from J. Brady glucose parameters unless noted. REMARKS These should be sufficient for refinement. REMARKS Additions 6-March-1992 Bill Weis REMARKS New atom types CCA, CCE, OA for the C1 & O1 positions to account REMARKS for different bond and angle values due to the anomeric effect. REMARKS More accurate equilibrium values for bond angle around this oxygen REMARKS in glycosidic linkages. CCE for equatorial O1, CCA for REMAKRS axial O1. For free sugar, keep OH1 as O1 atomtype; changed to OA REMARKS for linkages. REMARKS References: G.A. Jeffrey (1990) Acta Cryst B46, 89-103; REMARKS K. Hirotsu & A.Shimada, (1974) Bull. Chem. Soc. Japan, 47, 1872-1879. REMARKS This set has been modified to be roughly consistent with REMARKS the csd-derived protein parameters of Engh and Huber. REMARKS New atom type CC6 for exocyclic 6 carbon REMARKS Bill Weis 5/11/92 set echo=false end checkversion 1.2 {bond force constants 6x previous. Some adjustments made to equilbrium values } bond CC OE 1780.2 1.438 ! closer to crystal structures bond CCE OE 1780.2 1.428 bond CCA OE 1780.2 1.419 bond CC CC 1284.0 1.526 ! adjusted to Jeffries bond CC CC6 1284.0 1.516 bond CCE CC 1284.0 1.526 bond CCA CC 1284.0 1.526 bond CC HA 337.3 1.099 bond CC6 HA 337.3 1.099 bond CCE HA 337.3 1.099 bond CCA HA 337.3 1.099 bond CC OH1 2005.8 1.420 bond CC6 OH1 2005.8 1.420 bond CCE OH1 2005.8 1.385 !force constant as for other exocylic OH bond CCA OH1 2005.8 1.398 ! " " " " " " " bond CCE OA 2005.8 1.385 ! " " " " " " " bond CCA OA 2005.8 1.398 ! " " " " " " " { Note elongated non-anomeric C-O bond for bridges } bond CC OA 2005.8 1.44 !force constant as for other exocylic OH bond CC6 OA 2005.8 1.44 bond CC NH1 2631.111 1.45 !as extended atom carbon-N bond CCE NH1 2631.111 1.45 !as extended atom carbon-N bond CCA NH1 2631.111 1.45 !as extended atom carbon-N bond CC C 1342.404 1.52 !" " " " -C bond CCE C 1342.404 1.52 bond CCA C 1342.404 1.52 {Angle force constants increased 10x, except angle around bridging link oxygen increased 5x } angle H OH1 CC 53.62 109.35 angle H OH1 CC6 53.62 109.35 angle H OH1 CCE 53.62 109.35 angle H OH1 CCA 53.62 109.35 angle HA CC HA 33.58 107.85 angle HA CC6 HA 33.58 107.85 angle HA CC CC 43.04 108.72 angle HA CC6 CC 43.04 108.72 angle HA CC CC6 43.04 108.72 angle HA CC CCE 43.04 108.72 angle HA CC CCA 43.04 108.72 angle HA CCE CC 43.04 108.72 angle HA CCA CC 43.04 108.72 angle HA CC OH1 45.89 109.89 angle HA CC6 OH1 45.89 109.89 angle HA CCE OH1 45.89 109.89 angle HA CCA OH1 45.89 109.89 angle HA CC OA 45.89 109.89 angle HA CC6 OA 45.89 109.89 angle HA CCE OA 45.89 109.89 angle HA CCA OA 45.89 109.89 angle HA CC OE 45.16 107.24 angle HA CCE OE 45.16 107.24 angle HA CCA OE 45.16 107.24 angle CC CC CC 380.3 110.40 angle CC CC CC6 380.3 112.50 angle CCE CC CC 380.3 110.40 angle CCA CC CC 380.3 110.40 angle CC CC6 OH1 756.8 111.20 angle CC CCE OH1 756.8 109.70 angle CC CCA OH1 756.8 109.70 angle CCE CC OH1 756.8 109.70 angle CCA CC OH1 756.8 109.70 angle CC CC OH1 756.8 109.70 angle CC CC OE 809.5 110.00 angle CC6 CC OE 809.5 107.20 angle CC CCE OE 809.5 110.00 angle CC CCA OE 809.5 110.00 angle CC CC OA 809.5 109.70 angle CC CC6 OA 809.5 109.70 !guess for 1-6 links angle CC CCE OA 809.5 109.70 angle CC CCA OA 809.5 109.70 angle CCE CC OA 809.5 109.70 angle CCA CC OA 809.5 109.70 !angle OE CC OH1 925.6 111.55 !angle OE CC OE 925.6 110.70 { C5 - O5 - C1 } angle CC OE CCE 906.9 112.0 angle CC OE CCA 906.9 114.0 { O5 - C1 - O1 } angle OE CCE OH1 925.6 108.0 angle OE CCE OA 925.6 108.0 angle OE CCA OH1 925.6 112.1 angle OE CCA OA 925.6 112.1 { bridge angle - note a fairly large spread in the literature, axial generally smaller than equatorial. Increased only 5x to reflect limited data} angle CCE OA CC 453.45 116. angle CCA OA CC 453.45 115. angle CCE OA CC6 453.45 116. !angle CCA OA CC6 453.45 115. angle CCA OA CC6 453.45 111.5 !alpha 1,6 link angle O C CC 850. 120. !Mo & Jensen, Acta B, 31, 2867 (1975), 8/30/93 angle C CC HA 70. 109.5 ! 8/30/93 { The following are guesses, generally by analogy to extended atom Carbons. } { Note equilibrium values not based on crystal structures. } angle CC CC NH1 650.0 110.0 angle CCE CC NH1 650.0 110.0 angle CCA CC NH1 650.0 110.0 angle CC CCE NH1 650.0 110.0 angle CC CCA NH1 650.0 110.0 angle HA CC NH1 45.0 109.5 angle HA CCE NH1 45.0 109.5 angle HA CCA NH1 45.0 109.5 angle CC NH1 H 35.0 120.0 angle CCE NH1 H 35.0 120.0 angle CCA NH1 H 35.0 120.0 angle CC NH1 C 775.0 120.0 angle CCE NH1 C 775.0 120.0 angle CCA NH1 C 775.0 120.0 angle NH1 CC OE 750.0 110.7 !A complete guess angle NH1 CCE OE 750.0 110.7 !A complete guess angle NH1 CCA OE 750.0 110.7 !A complete guess angle NH1 C CC 200.0 117.5 angle C CCE OH1 700.0 109.5 !A complete guess for SIA O2 angle C CCA OH1 700.0 109.5 !A complete guess for SIA O2 angle C CCE OA 700.0 109.5 !A complete guess for SIA O2 angle C CCA OA 700.0 109.5 !A complete guess for SIA O2 angle O C CCE 850.0 121.5 angle O C CCA 850.0 121.5 angle C CCE HA 70.0 109.5 angle C CCA HA 70.0 109.5 { This is (360-the usual OC-C-OC angle of 122.5)/2 } angle CCE C OC 850.0 118.75 angle CCA C OC 850.0 118.75 { Use the same angles to HA in the C1 position of NANA } angle C CCE OE 850.0 107.24 angle C CCA OE 850.0 107.24 angle C CCE CC 700.0 108.72 angle C CCA CC 700.0 108.72 dihedral X CC CC X 3.0630 3 0.0 dihedral X CC CC6 X 3.0630 3 0.0 dihedral X CCE CC X 3.0630 3 0.0 dihedral X CCA CC X 3.0630 3 0.0 dihedral X CC OH1 X 1.3293 3 0.0 dihedral X CC6 OH1 X 1.3293 3 0.0 dihedral X CCE OH1 X 1.3293 3 0.0 dihedral X CCA OH1 X 1.3293 3 0.0 dihedral X CC OA X 1.3293 3 0.0 dihedral X CC6 OA X 1.3293 3 0.0 dihedral X CCE OA X 1.3293 3 0.0 dihedral X CCA OA X 1.3293 3 0.0 dihedral X CC OE X 2.7834 3 0.0 dihedral X CCE OE X 2.7834 3 0.0 dihedral X CCA OE X 2.7834 3 0.0 { The following are guesses, generally by analogy to extended atom Carbons } dihedral HA CC NH1 H 0.3 3 180.0 !for NAG and NANA dihedral X CC NH1 X 0.9 3 0.0 !beta link to Asn Nd1 dihedral X CCE NH1 X 0.9 3 0.0 !beta link to Asn Nd1 dihedral X CCA NH1 X 0.9 3 0.0 !beta link to Asn Nd1 dihedral X C CCE X 0.0 3 0.0 dihedral X C CCA X 0.0 3 0.0 dihedral X C CC X 0.0 3 0.0 ! N-acetyl in NAG, 8/30/93 dihedral CC NH1 C CC 5.0 2 0.0 ! peptide plane in NAG ! guess - PDA 8/99 { These high force constants maintain chiral centers on the rings } improper CC X X CC 300.0 0 35.26439 improper CCE X X CC 300.0 0 35.26439 improper CCA X X CC 300.0 0 35.26439 improper OH1 X X CC 300.0 0 35.26439 improper OH1 X X CCE 300.0 0 35.26439 improper OH1 X X CCA 300.0 0 35.26439 improper OA X X CC 300.0 0 35.26439 improper OA X X CCE 300.0 0 35.26439 improper OA X X CCA 300.0 0 35.26439 improper CC X X OE 300.0 0 35.26439 improper CCE X X OE 300.0 0 35.26439 improper CCA X X OE 300.0 0 35.26439 { This is as other acids } improper C X X CCE 300.0 0 0.0 !NANA acid planarity improper C X X CCA 300.0 0 0.0 !NANA acid planarity !!for use with: !!NBXMOD=5 ATOM CDIEL SHIFT vswitch !! CUTNB=8.0 CTOFNB=7.5 CTONNB=6.5 EPS=1.0 E14FAC=0.4 WMIN=1.5 !NONBonded HA 0.0045 2.6157 0.0045 2.6157 NONBonded CC 0.0903 3.2072 0.0903 3.2072 NONBonded CC6 0.0903 3.2072 0.0903 3.2072 NONBonded CCE 0.0903 3.2072 0.0903 3.2072 NONBonded CCA 0.0903 3.2072 0.0903 3.2072 NONBonded OE 0.1591 2.8509 0.1591 2.8509 NONBonded OA 0.1591 2.8509 0.1591 2.8509 set echo=true end