REMARKS toppar/carbohydrate.top {pyranose sugar toplogoy for crystallographic remarks structure determination} REMARKS FOR USE WITH CARBOHYDRATE.PARAM AND protein_rep.param PROTEIN PARAMETERS REMARKS ========================================================== REMARKS Bill Weis 10-July-1988 REMARKS Also see CARBOHYDRATE.PARAM for parameters. REMARKS Charges taken from John Brady's glucose topology file for ring, REMARKS others from protein parameter file. REMARKS Idealized values for impropers at ring carbons to allow simple REMARKS construction of various anomers/epimers. REMARKS Any other hexose or link can be easily constructed by analogy to these. REMARKS Additions 6-March-1992 Bill Weis for use with PARAM2.CHO 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 Additional CC6 atomtype for exocyclic carbon 5/11/92 set echo=false end checkversion 1.2 AUTOGENERATE ANGLES=TRUE END {*===========================*} {default masses -- only those not in protein topology TOPH19X.PRO} MASS CC 12.01100! carbohydrate carbon MASS CC6 12.01100! carbohydrate carbon, exocyclic C6 MASS CCE 12.01100! carbohydrate carbon, equatorial C1 MASS CCA 12.01100! carbohydrate carbon, axial C1 MASS OE 15.99940! ether oxygen MASS OA 15.99940! ether oxygen in glycosidic bond MASS H 1.00800! hydrogen MASS HA 1.00800! aliphatic hydrogen RESIdue GLC !beta-d-glucose, pyranose form GROUP ATOM C1 TYPE=CCE CHARge= 0.350 END ATOM H1 TYPE=HA CHARge= 0.100 END ATOM O1 TYPE=OH1 CHARge=-0.650 END ATOM HO1 TYPE=H CHARge= 0.400 END ATOM C2 TYPE=CC CHARge= 0.150 END ATOM O2 TYPE=OH1 CHARge=-0.650 END ATOM H2 TYPE=HA CHARge= 0.100 END ATOM HO2 TYPE=H CHARge= 0.400 END ATOM C3 TYPE=CC CHARge= 0.150 END ATOM H3 TYPE=HA CHARge= 0.100 END ATOM O3 TYPE=OH1 CHARge=-0.650 END ATOM HO3 TYPE=H CHARge= 0.400 END ATOM C4 TYPE=CC CHARge= 0.150 END ATOM H4 TYPE=HA CHARge= 0.100 END ATOM O4 TYPE=OH1 CHARge=-0.650 END ATOM HO4 TYPE=H CHARge= 0.400 END ATOM C5 TYPE=CC CHARge= 0.100 END ATOM H5 TYPE=HA CHARge= 0.100 END ATOM O5 TYPE=OE CHARge=-0.400 END ATOM C6 TYPE=CC6 CHARge= 0.050 END ATOM H61 TYPE=HA CHARge= 0.100 END ATOM H62 TYPE=HA CHARge= 0.100 END ATOM O6 TYPE=OH1 CHARge=-0.650 END ATOM HO6 TYPE=H CHARge= 0.400 END BOND C1 O1 BOND C1 H1 BOND O1 HO1 BOND C1 O5 BOND C1 C2 BOND C2 H2 BOND C2 O2 BOND O2 HO2 BOND C2 C3 BOND C3 H3 BOND C3 O3 BOND O3 HO3 BOND C3 C4 BOND C4 H4 BOND C4 O4 BOND O4 HO4 BOND C4 C5 BOND C5 H5 BOND C5 C6 BOND C6 H61 BOND C6 H62 BOND C6 O6 BOND O6 HO6 BOND C5 O5 DIHEDRAL C1 C2 C3 C4 DIHEDRAL C2 C3 C4 C5 DIHEDRAL C3 C4 C5 O5 DIHEDRAL C4 C5 O5 C1 DIHEDRAL C5 O5 C1 C2 DIHEDRAL O5 C1 C2 C3 DIHEDRAL H1 C1 O1 HO1 DIHEDRAL H2 C2 O2 HO2 DIHEDRAL H3 C3 O3 HO3 DIHEDRAL H4 C4 O4 HO4 DIHEDRAL H5 C5 C6 O6 DIHEDRAL C5 C6 O6 H61 IMPRoper C1 O5 H1 C2 ! IMPRoper C1 O1 O5 C2 IMPRoper C2 C1 O2 C3 IMPRoper C3 O3 C2 C4 IMPRoper C4 C3 O4 C5 IMPRoper C5 C6 C4 O5 END RESIdue GAL !beta-d-galactose, pyranose form GROUP ATOM C1 TYPE=CCE CHARge= 0.350 END ATOM H1 TYPE=HA CHARge= 0.100 END ATOM O1 TYPE=OH1 CHARge=-0.650 END ATOM HO1 TYPE=H CHARge= 0.400 END ATOM C2 TYPE=CC CHARge= 0.150 END ATOM O2 TYPE=OH1 CHARge=-0.650 END ATOM H2 TYPE=HA CHARge= 0.100 END ATOM HO2 TYPE=H CHARge= 0.400 END ATOM C3 TYPE=CC CHARge= 0.150 END ATOM H3 TYPE=HA CHARge= 0.100 END ATOM O3 TYPE=OH1 CHARge=-0.650 END ATOM HO3 TYPE=H CHARge= 0.400 END ATOM C4 TYPE=CC CHARge= 0.150 END ATOM H4 TYPE=HA CHARge= 0.100 END ATOM O4 TYPE=OH1 CHARge=-0.650 END ATOM HO4 TYPE=H CHARge= 0.400 END ATOM C5 TYPE=CC CHARge= 0.100 END ATOM H5 TYPE=HA CHARge= 0.100 END ATOM O5 TYPE=OE CHARge=-0.400 END ATOM C6 TYPE=CC6 CHARge= 0.050 END ATOM H61 TYPE=HA CHARge= 0.100 END ATOM H62 TYPE=HA CHARge= 0.100 END ATOM O6 TYPE=OH1 CHARge=-0.650 END ATOM HO6 TYPE=H CHARge= 0.400 END BOND C1 O1 BOND C1 H1 BOND O1 HO1 BOND C1 O5 BOND C1 C2 BOND C2 H2 BOND C2 O2 BOND O2 HO2 BOND C2 C3 BOND C3 H3 BOND C3 O3 BOND O3 HO3 BOND C3 C4 BOND C4 H4 BOND C4 O4 BOND O4 HO4 BOND C4 C5 BOND C5 H5 BOND C5 C6 BOND C6 H61 BOND C6 H62 BOND C6 O6 BOND O6 HO6 BOND C5 O5 DIHEDRAL C1 C2 C3 C4 DIHEDRAL C2 C3 C4 C5 DIHEDRAL C3 C4 C5 O5 DIHEDRAL C4 C5 O5 C1 DIHEDRAL C5 O5 C1 C2 DIHEDRAL O5 C1 C2 C3 DIHEDRAL H1 C1 O1 HO1 DIHEDRAL H2 C2 O2 HO2 DIHEDRAL H3 C3 O3 HO3 DIHEDRAL H4 C4 O4 HO4 DIHEDRAL H5 C5 C6 O6 DIHEDRAL C5 C6 O6 H61 IMPRoper C1 O1 O5 C2 IMPRoper C2 C1 O2 C3 IMPRoper C3 O3 C2 C4 IMPRoper C4 O4 C3 C5 {Axial C4} IMPRoper C5 C6 C4 O5 END RESIdue MAN !beta-d-mannose, pyranose form GROUP ATOM C1 TYPE=CCE CHARge= 0.350 END ATOM H1 TYPE=HA CHARge= 0.100 END ATOM O1 TYPE=OH1 CHARge=-0.650 END ATOM HO1 TYPE=H CHARge= 0.400 END ATOM C2 TYPE=CC CHARge= 0.150 END ATOM O2 TYPE=OH1 CHARge=-0.650 END ATOM H2 TYPE=HA CHARge= 0.100 END ATOM HO2 TYPE=H CHARge= 0.400 END ATOM C3 TYPE=CC CHARge= 0.150 END ATOM H3 TYPE=HA CHARge= 0.100 END ATOM O3 TYPE=OH1 CHARge=-0.650 END ATOM HO3 TYPE=H CHARge= 0.400 END ATOM C4 TYPE=CC CHARge= 0.150 END ATOM H4 TYPE=HA CHARge= 0.100 END ATOM O4 TYPE=OH1 CHARge=-0.650 END ATOM HO4 TYPE=H CHARge= 0.400 END ATOM C5 TYPE=CC CHARge= 0.100 END ATOM H5 TYPE=HA CHARge= 0.100 END ATOM O5 TYPE=OE CHARge=-0.400 END ATOM C6 TYPE=CC6 CHARge= 0.050 END ATOM H61 TYPE=HA CHARge= 0.100 END ATOM H62 TYPE=HA CHARge= 0.100 END ATOM O6 TYPE=OH1 CHARge=-0.650 END ATOM HO6 TYPE=H CHARge= 0.400 END BOND C1 O1 BOND C1 H1 BOND O1 HO1 BOND C1 O5 BOND C1 C2 BOND C2 H2 BOND C2 O2 BOND O2 HO2 BOND C2 C3 BOND C3 H3 BOND C3 O3 BOND O3 HO3 BOND C3 C4 BOND C4 H4 BOND C4 O4 BOND O4 HO4 BOND C4 C5 BOND C5 H5 BOND C5 C6 BOND C6 H61 BOND C6 H62 BOND C6 O6 BOND O6 HO6 BOND C5 O5 DIHEDRAL C1 C2 C3 C4 DIHEDRAL C2 C3 C4 C5 DIHEDRAL C3 C4 C5 O5 DIHEDRAL C4 C5 O5 C1 DIHEDRAL C5 O5 C1 C2 DIHEDRAL O5 C1 C2 C3 DIHEDRAL H1 C1 O1 HO1 DIHEDRAL H2 C2 O2 HO2 DIHEDRAL H3 C3 O3 HO3 DIHEDRAL H4 C4 O4 HO4 DIHEDRAL H5 C5 C6 O6 DIHEDRAL C5 C6 O6 H61 IMPRoper C1 O5 H1 C2 ! IMPRoper C1 O1 O5 C2 IMPRoper C2 O2 C1 C3 {axial C2} IMPRoper C3 O3 C2 C4 IMPRoper C4 C3 O4 C5 IMPRoper C5 C6 C4 O5 END RESIdue NAG !2-N-Acetyl-beta-d-glucose, pyranose form GROUP ATOM C1 TYPE=CCE CHARge= 0.350 END ATOM H1 TYPE=HA CHARge= 0.100 END ATOM O1 TYPE=OH1 CHARge=-0.650 END ATOM HO1 TYPE=H CHARge= 0.400 END ATOM C2 TYPE=CC CHARge= 0.000 END ATOM H2 TYPE=HA CHARge= 0.100 END ATOM N2 TYPE=NH1 CHARge=-0.350 END ATOM HN2 TYPE=H CHARge= 0.250 END ATOM C7 TYPE=C CHARge= 0.550 END ATOM O7 TYPE=O CHARge=-0.550 END ATOM C8 TYPE=CC CHARge=-0.300 END ATOM H81 TYPE=HA CHARge= 0.100 END ATOM H82 TYPE=HA CHARge= 0.100 END ATOM H83 TYPE=HA CHARge= 0.100 END ATOM C3 TYPE=CC CHARge= 0.150 END ATOM H3 TYPE=HA CHARge= 0.100 END ATOM O3 TYPE=OH1 CHARge=-0.650 END ATOM HO3 TYPE=H CHARge= 0.400 END ATOM C4 TYPE=CC CHARge= 0.150 END ATOM H4 TYPE=HA CHARge= 0.100 END ATOM O4 TYPE=OH1 CHARge=-0.650 END ATOM HO4 TYPE=H CHARge= 0.400 END ATOM C5 TYPE=CC CHARge= 0.100 END ATOM H5 TYPE=HA CHARge= 0.100 END ATOM O5 TYPE=OE CHARge=-0.400 END ATOM C6 TYPE=CC6 CHARge= 0.050 END ATOM H61 TYPE=HA CHARge= 0.100 END ATOM H62 TYPE=HA CHARge= 0.100 END ATOM O6 TYPE=OH1 CHARge=-0.650 END ATOM HO6 TYPE=H CHARge= 0.400 END BOND C1 O1 BOND C1 H1 BOND O1 HO1 BOND C1 O5 BOND C1 C2 BOND C2 H2 BOND C2 N2 BOND N2 HN2 BOND N2 C7 BOND C7 O7 BOND C7 C8 BOND C8 H81 BOND C8 H82 BOND C8 H83 BOND C2 C3 BOND C3 H3 BOND C3 O3 BOND O3 HO3 BOND C3 C4 BOND C4 H4 BOND C4 O4 BOND O4 HO4 BOND C4 C5 BOND C5 H5 BOND C5 C6 BOND C6 H61 BOND C6 H62 BOND C6 O6 BOND O6 HO6 BOND C5 O5 DIHEDRAL C1 C2 C3 C4 DIHEDRAL C2 C3 C4 C5 DIHEDRAL C3 C4 C5 O5 DIHEDRAL C4 C5 O5 C1 DIHEDRAL C5 O5 C1 C2 DIHEDRAL O5 C1 C2 C3 DIHEDRAL H1 C1 O1 HO1 DIHEDRAL H2 C2 N2 HN2 DIHEDRAL C2 N2 C7 C8 DIHEDRAL N2 C7 C8 H81 DIHEDRAL H3 C3 O3 HO3 DIHEDRAL H4 C4 O4 HO4 DIHEDRAL H5 C5 C6 O6 DIHEDRAL C5 C6 O6 H61 IMPRoper C1 O5 H1 C2 ! IMPRoper C1 O1 O5 C2 IMPRoper C2 C1 N2 C3 IMPRoper N2 C7 C2 HN2 {planar N} IMPRoper C7 C8 N2 O7 {planar C} IMPRoper C3 O3 C2 C4 IMPRoper C4 C3 O4 C5 IMPRoper C5 C6 C4 O5 END RESIdue FUC !L-fucose, pyranose form GROUP ATOM C1 TYPE=CCE CHARge= 0.350 END ATOM H1 TYPE=HA CHARge= 0.100 END ATOM O1 TYPE=OH1 CHARge=-0.650 END ATOM HO1 TYPE=H CHARge= 0.400 END ATOM C2 TYPE=CC CHARge= 0.150 END ATOM O2 TYPE=OH1 CHARge=-0.650 END ATOM H2 TYPE=HA CHARge= 0.100 END ATOM HO2 TYPE=H CHARge= 0.400 END ATOM C3 TYPE=CC CHARge= 0.150 END ATOM H3 TYPE=HA CHARge= 0.100 END ATOM O3 TYPE=OH1 CHARge=-0.650 END ATOM HO3 TYPE=H CHARge= 0.400 END ATOM C4 TYPE=CC CHARge= 0.150 END ATOM H4 TYPE=HA CHARge= 0.100 END ATOM O4 TYPE=OH1 CHARge=-0.650 END ATOM HO4 TYPE=H CHARge= 0.400 END ATOM C5 TYPE=CC CHARge= 0.100 END ATOM H5 TYPE=HA CHARge= 0.100 END ATOM O5 TYPE=OE CHARge=-0.400 END ATOM C6 TYPE=CC6 CHARge=-0.300 END ATOM H61 TYPE=HA CHARge= 0.100 END ATOM H62 TYPE=HA CHARge= 0.100 END ATOM H63 TYPE=HA CHARge= 0.100 END BOND C1 O1 BOND C1 H1 BOND O1 HO1 BOND C1 O5 BOND C1 C2 BOND C2 H2 BOND C2 O2 BOND O2 HO2 BOND C2 C3 BOND C3 H3 BOND C3 O3 BOND O3 HO3 BOND C3 C4 BOND C4 H4 BOND C4 O4 BOND O4 HO4 BOND C4 C5 BOND C5 H5 BOND C5 C6 BOND C6 H61 BOND C6 H62 BOND C6 H63 BOND C5 O5 DIHEDRAL C1 C2 C3 C4 DIHEDRAL C2 C3 C4 C5 DIHEDRAL C3 C4 C5 O5 DIHEDRAL C4 C5 O5 C1 DIHEDRAL C5 O5 C1 C2 DIHEDRAL O5 C1 C2 C3 DIHEDRAL H1 C1 O1 HO1 DIHEDRAL H2 C2 O2 HO2 DIHEDRAL H3 C3 O3 HO3 DIHEDRAL H4 C4 O4 HO4 DIHEDRAL H5 C5 C6 H61 { This is an L-sugar, so impropers are reversed to maintain ring } { geometry equivalent to D-hexoses } IMPRoper C1 H1 O5 C2 ! IMPRoper C1 O5 O1 C2 IMPRoper C2 O2 C1 C3 IMPRoper C3 C2 O3 C4 IMPRoper C4 C3 O4 C5 {Axial C4} IMPRoper C5 C4 C6 O5 END RESIdue SIA {alpha-N-acetyl neuraminic acid} GROUP ATOM C1 TYPE=C CHARge= 0.360 END ATOM O1A TYPE=OC CHARge=-0.600 END ATOM O1B TYPE=OC CHARge=-0.600 END ATOM C2 TYPE=CCE CHARge= 0.290 END ATOM O2 TYPE=OH1 CHARge=-0.650 END ATOM HO2 TYPE=H CHARge= 0.400 END ATOM C3 TYPE=CC CHARge=-0.200 END ATOM H31 TYPE=HA CHARge= 0.100 END ATOM H32 TYPE=HA CHARge= 0.100 END ATOM C4 TYPE=CC CHARge= 0.150 END ATOM H4 TYPE=HA CHARge= 0.100 END ATOM O4 TYPE=OH1 CHARge=-0.650 END ATOM HO4 TYPE=H CHARge= 0.400 END ATOM C5 TYPE=CC CHARge= 0.000 END ATOM H5 TYPE=HA CHARge= 0.100 END ATOM N5 TYPE=NH1 CHARge=-0.350 END ATOM HN5 TYPE=H CHARge= 0.250 END ATOM C10 TYPE=C CHARge= 0.550 END ATOM O10 TYPE=O CHARge=-0.550 END ATOM C11 TYPE=CC CHARge=-0.300 END ATOM H111 TYPE=HA CHARge= 0.100 END ATOM H112 TYPE=HA CHARge= 0.100 END ATOM H113 TYPE=HA CHARge= 0.100 END ATOM C6 TYPE=CC CHARge= 0.100 END ATOM H6 TYPE=HA CHARge= 0.100 END ATOM O6 TYPE=OE CHARge=-0.400 END ATOM C7 TYPE=CC CHARge= 0.150 END ATOM H7 TYPE=HA CHARge= 0.100 END ATOM O7 TYPE=OH1 CHARge=-0.650 END ATOM HO7 TYPE=H CHARge= 0.400 END ATOM C8 TYPE=CC CHARge= 0.150 END ATOM H8 TYPE=HA CHARge= 0.100 END ATOM O8 TYPE=OH1 CHARge=-0.650 END ATOM HO8 TYPE=H CHARge= 0.400 END ATOM C9 TYPE=CC CHARge= 0.050 END ATOM H91 TYPE=HA CHARge= 0.100 END ATOM H92 TYPE=HA CHARge= 0.100 END ATOM O9 TYPE=OH1 CHARge=-0.650 END ATOM HO9 TYPE=H CHARge= 0.400 END BOND C1 O1A BOND C1 O1B BOND C1 C2 BOND C2 O2 BOND O2 HO2 BOND C2 O6 BOND C2 C3 BOND C3 H31 BOND C3 H32 BOND C3 C4 BOND C4 H4 BOND C4 O4 BOND O4 HO4 BOND C4 C5 BOND C5 H5 BOND C5 N5 BOND N5 HN5 BOND N5 C10 BOND C10 O10 BOND C10 C11 BOND C11 H111 BOND C11 H112 BOND C11 H113 BOND C5 C6 BOND C6 H6 BOND C6 C7 BOND C7 H7 BOND C7 O7 BOND O7 HO7 BOND C7 C8 BOND C8 H8 BOND C8 O8 BOND O8 HO8 BOND C8 C9 BOND C9 H91 BOND C9 H92 BOND C9 O9 BOND O9 HO9 BOND C6 O6 DIHEDRAL C2 C3 C4 C5 DIHEDRAL C3 C4 C5 C6 DIHEDRAL C4 C5 C6 O6 DIHEDRAL C5 C6 O6 C2 DIHEDRAL O6 C2 C3 C4 DIHEDRAL C1 C2 O2 HO2 DIHEDRAL O2 C2 C1 O1A DIHEDRAL H4 C4 O4 HO4 DIHEDRAL H5 C5 N5 HN5 DIHEDRAL C5 N5 C10 C11 DIHEDRAL N5 C10 C11 H111 DIHEDRAL H6 C6 C7 C8 DIHEDRAL H6 C6 C7 O7 DIHEDRAL C6 C7 C8 C9 DIHEDRAL C6 C7 C8 O8 DIHEDRAL C7 C8 C9 O9 DIHEDRAL C8 C9 O9 HO9 { This is an L-sugar, so impropers are reversed to maintain ring } { geometry equivalent to D-hexoses } IMPRoper C1 O1A O1B C2 !planar acid IMPRoper C2 C1 O6 C3 {axial acid, i.e. alpha configuration} ! IMPRoper C2 O6 O2 C3 IMPRoper C3 H31 C2 C4 IMPRoper C4 C3 O4 C5 IMPRoper C5 N5 C4 C6 IMPRoper N5 C10 C5 HN5 !planar N-acetyl N IMPRoper C10 C11 N5 O10 !planar N-acetyl C IMPRoper C6 C5 C7 O6 IMPRoper C7 C6 O7 C8 IMPRoper C8 C7 O8 C9 END RESIdue XYL !beta-d-xylose, pyranose form GROUP ATOM C1 TYPE=CCE CHARge= 0.350 END ATOM H1 TYPE=HA CHARge= 0.100 END ATOM O1 TYPE=OH1 CHARge=-0.650 END ATOM HO1 TYPE=H CHARge= 0.400 END ATOM C2 TYPE=CC CHARge= 0.150 END ATOM O2 TYPE=OH1 CHARge=-0.650 END ATOM H2 TYPE=HA CHARge= 0.100 END ATOM HO2 TYPE=H CHARge= 0.400 END ATOM C3 TYPE=CC CHARge= 0.150 END ATOM H3 TYPE=HA CHARge= 0.100 END ATOM O3 TYPE=OH1 CHARge=-0.650 END ATOM HO3 TYPE=H CHARge= 0.400 END ATOM C4 TYPE=CC CHARge= 0.150 END ATOM H4 TYPE=HA CHARge= 0.100 END ATOM O4 TYPE=OH1 CHARge=-0.650 END ATOM HO4 TYPE=H CHARge= 0.400 END ATOM C5 TYPE=CC CHARge= 0.100 END ATOM O5 TYPE=OE CHARge=-0.400 END ATOM H51 TYPE=HA CHARge= 0.100 END ATOM H52 TYPE=HA CHARge= 0.100 END BOND C1 O1 BOND C1 H1 BOND O1 HO1 BOND C1 O5 BOND C1 C2 BOND C2 H2 BOND C2 O2 BOND O2 HO2 BOND C2 C3 BOND C3 H3 BOND C3 O3 BOND O3 HO3 BOND C3 C4 BOND C4 H4 BOND C4 O4 BOND O4 HO4 BOND C4 C5 BOND C5 H51 BOND C5 H52 BOND C5 O5 DIHEDRAL C1 C2 C3 C4 DIHEDRAL C2 C3 C4 C5 DIHEDRAL C3 C4 C5 O5 DIHEDRAL C4 C5 O5 C1 DIHEDRAL C5 O5 C1 C2 DIHEDRAL O5 C1 C2 C3 DIHEDRAL H1 C1 O1 HO1 DIHEDRAL H2 C2 O2 HO2 DIHEDRAL H3 C3 O3 HO3 DIHEDRAL H4 C4 O4 HO4 IMPRoper C1 O5 H1 C2 IMPRoper C1 O1 O5 C2 IMPRoper C2 C1 O2 C3 {equatorial C2} IMPRoper C3 O3 C2 C4 IMPRoper C4 C3 O4 C5 IMPRoper C5 H51 C4 O5 END PRESidue BtoA {beta to alpha d-pyranose patch} DELEte IMPRoper C1 O5 H1 C2 ADD IMPRoper C1 H1 O5 C2 END { For the following link patches, the anomer is determined by the link } { patch, assuming that the input residue is the BETA anomer } PRESidue B1N {beta link from C1 to Asn Nd2} MODIfy ATOM +ND2 TYPE=NH1 CHARge=-0.35 END MODIfy ATOM +HD22 CHARge= 0.25 END DELEte ATOM +HD21 END MODIfy ATOM -C1 CHARge= 0.20 END DELEte ATOM -O1 END DELEte ATOM -HO1 END ADD BOND -C1 +ND2 ADD ANGLe +CG +ND2 -C1 ADD ANGLe +HD22 +ND2 -C1 ADD ANGLe +ND2 -C1 -C2 ADD ANGLe +ND2 -C1 -O5 ADD ANGLe +ND2 -C1 -H1 !ADD DIHEdral +CB +CG +ND2 -C1 !trans peptide bond !ADD DIHEdral +CG +ND2 -C1 -C2 !ADD DIHEdral +CG +ND2 -C1 -O5 ADD DIHEdral +CG +ND2 -C1 -H1 {respecify planar ND2 as removed HD21 above } { Note that we take this from the protein parameter file NH1 X X C, which has } { a stronger restraint on this (for peptide planes) than the Asn side chain } ADD IMPRoper +ND2 -C1 +HD22 +CG { We keep the sugar C1 beta, no need to define or modify impropers } END PRESidue B12 {beta(1,2) link} MODIfy ATOM +O2 TYPE=OA CHARge=-0.40 END MODIfy ATOM +C2 CHARge= 0.10 END DELEte ATOM +HO2 END MODIfy ATOM -C1 CHARge= 0.30 END DELEte ATOM -O1 END DELEte ATOM -HO1 END ADD BOND -C1 +O2 ADD ANGle +C2 +O2 -C1 ADD ANGle +O2 -C1 -H1 ADD ANGle +O2 -C1 -O5 ADD ANGle +O2 -C1 -C2 ADD DIHEdral +C2 +O2 -C1 -H1 ADD DIHEdral +C2 +O2 -C1 -O5 ADD DIHEdral +C2 +O2 -C1 -C2 END PRESidue B14 {beta(1,4) link} MODIfy ATOM +O4 TYPE=OA CHARge=-0.40 END MODIfy ATOM +C4 CHARge= 0.10 END DELEte ATOM +HO4 END MODIfy ATOM -C1 CHARge= 0.30 END DELEte ATOM -O1 END DELEte ATOM -HO1 END ADD BOND -C1 +O4 ADD ANGle +C4 +O4 -C1 ADD ANGle +O4 -C1 -H1 ADD ANGle +O4 -C1 -O5 ADD ANGle +O4 -C1 -C2 ADD DIHEdral +C4 +O4 -C1 -H1 ADD DIHEdral +C4 +O4 -C1 -O5 ADD DIHEdral +C4 +O4 -C1 -C2 END PRESidue A12 {alpha(1,2) link} MODIfy ATOM +O2 TYPE=OA CHARge=-0.40 END MODIfy ATOM +C2 CHARge= 0.10 END DELEte ATOM +HO2 END MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END DELEte ATOM -O1 END DELEte ATOM -HO1 END ADD BOND -C1 +O2 ADD ANGle +C2 +O2 -C1 ADD ANGle +O2 -C1 -H1 ADD ANGle +O2 -C1 -O5 ADD ANGle +O2 -C1 -C2 ADD DIHEdral +C2 +O2 -C1 -H1 ADD DIHEdral +C2 +O2 -C1 -O5 ADD DIHEdral +C2 +O2 -C1 -C2 { put C1 in the alpha configuration} DELETE IMPRoper -C1 -O5 -H1 -C2 ADD IMPRoper -C1 -H1 -O5 -C2 END PRESidue A13 {alpha(1,3) link} MODIfy ATOM +O3 TYPE=OA CHARge=-0.40 END MODIfy ATOM +C3 CHARge= 0.10 END DELEte ATOM +HO3 END MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END DELEte ATOM -O1 END DELEte ATOM -HO1 END ADD BOND -C1 +O3 ADD ANGle +C3 +O3 -C1 ADD ANGle +O3 -C1 -H1 ADD ANGle +O3 -C1 -O5 ADD ANGle +O3 -C1 -C2 ADD DIHEdral +C3 +O3 -C1 -H1 ADD DIHEdral +C3 +O3 -C1 -O5 ADD DIHEdral +C3 +O3 -C1 -C2 { put C1 in the alpha configuration} DELETE IMPRoper -C1 -O5 -H1 -C2 ADD IMPRoper -C1 -H1 -O5 -C2 END ! added 11/27/96 PRESidue A12L { alpha(1,2) link for L-fucose } MODIfy ATOM +O2 TYPE=OA CHARge=-0.40 END MODIfy ATOM +C2 CHARge= 0.10 END DELEte ATOM +HO2 END MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END DELEte ATOM -O1 END DELEte ATOM -HO1 END ADD BOND -C1 +O2 ADD ANGle +C2 +O2 -C1 ADD ANGle +O2 -C1 -H1 ADD ANGle +O2 -C1 -O5 ADD ANGle +O2 -C1 -C2 ADD DIHEdral +C2 +O2 -C1 -H1 ADD DIHEdral +C2 +O2 -C1 -O5 ADD DIHEdral +C2 +O2 -C1 -C2 { put C1 in the alpha configuration} DELETE IMPRoper -C1 -H1 -O5 -C2 ADD IMPRoper -C1 -O5 -H1 -C2 END PRESidue A13L { alpha(1,3) link for L-fucose } MODIfy ATOM +O3 TYPE=OA CHARge=-0.40 END MODIfy ATOM +C3 CHARge= 0.00 END DELEte ATOM +HO3 END MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END DELEte ATOM -O1 END DELEte ATOM -HO1 END ADD BOND -C1 +O3 ADD ANGle +C3 +O3 -C1 ADD ANGle +O3 -C1 -H1 ADD ANGle +O3 -C1 -O5 ADD ANGle +O3 -C1 -C2 ADD DIHEdral +C3 +O3 -C1 -H1 ADD DIHEdral +C3 +O3 -C1 -O5 ADD DIHEdral +C3 +O3 -C1 -C2 { put C1 in the alpha configuration} DELETE IMPRoper -C1 -H1 -O5 -C2 ADD IMPRoper -C1 -O5 -H1 -C2 END PRESidue A14 {alpha(1,4) link} MODIfy ATOM +O4 TYPE=OA CHARge=-0.40 END MODIfy ATOM +C4 CHARge= 0.10 END DELEte ATOM +HO4 END MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END DELEte ATOM -O1 END DELEte ATOM -HO1 END ADD BOND -C1 +O4 ADD ANGle +C4 +O4 -C1 ADD ANGle +O4 -C1 -H1 ADD ANGle +O4 -C1 -O5 ADD ANGle +O4 -C1 -C2 ADD DIHEdral +C4 +O4 -C1 -H1 ADD DIHEdral +C4 +O4 -C1 -O5 ADD DIHEdral +C4 +O4 -C1 -C2 { put C1 in the alpha configuration} DELETE IMPRoper -C1 -O5 -H1 -C2 ADD IMPRoper -C1 -H1 -O5 -C2 END PRESidue A16 { alpha(1,6) link } MODIfy ATOM +O6 TYPE=OA CHARge=-0.40 END MODIfy ATOM +C6 CHARge= 0.00 END DELEte ATOM +HO6 END MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END DELEte ATOM -O1 END DELEte ATOM -HO1 END ADD BOND -C1 +O6 ADD ANGle +C6 +O6 -C1 ADD ANGle +O6 -C1 -H1 ADD ANGle +O6 -C1 -O5 ADD ANGle +O6 -C1 -C2 ADD DIHEdral +C6 +O6 -C1 -H1 ADD DIHEdral +C6 +O6 -C1 -O5 ADD DIHEdral +C6 +O6 -C1 -C2 { put C1 in the alpha configuration} DELETE IMPRoper -C1 -O5 -H1 -C2 ADD IMPRoper -C1 -H1 -O5 -C2 END PRESidue A16L { alpha(1,6) link for L-fucose } MODIfy ATOM +O6 TYPE=OA CHARge=-0.40 END MODIfy ATOM +C6 CHARge= 0.00 END DELEte ATOM +HO6 END MODIfy ATOM -C1 TYPE=CCA CHARge= 0.30 END DELEte ATOM -O1 END DELEte ATOM -HO1 END ADD BOND -C1 +O6 ADD ANGle +C6 +O6 -C1 ADD ANGle +O6 -C1 -H1 ADD ANGle +O6 -C1 -O5 ADD ANGle +O6 -C1 -C2 ADD DIHEdral +C6 +O6 -C1 -H1 ADD DIHEdral +C6 +O6 -C1 -O5 ADD DIHEdral +C6 +O6 -C1 -C2 { put C1 in the alpha configuration} DELETE IMPRoper -C1 -H1 -O5 -C2 ADD IMPRoper -C1 -O5 -H1 -C2 END {Links for sialic acid -- input anomer is assumed ALPHA, i.e. glycosidic } { oxygen is equatorial to the NANA ring } PRESidue A23 {alpha(2,3) link for NANA} MODIfy ATOM +O3 TYPE=OA CHARge=-0.40 END MODIfy ATOM +C3 CHARge= 0.10 END DELEte ATOM +HO3 END MODIfy ATOM -C2 CHARge= 0.24 END DELEte ATOM -O2 END DELEte ATOM -HO2 END ADD BOND -C2 +O3 ADD ANGle +C3 +O3 -C2 ADD ANGle +O3 -C2 -C1 ADD ANGle +O3 -C2 -O6 ADD ANGle +O3 -C2 -C3 ADD DIHEdral +C3 +O3 -C2 -C1 ADD DIHEdral +C3 +O3 -C2 -O6 ADD DIHEdral +C3 +O3 -C2 -C3 ADD DIHEdral +O3 -C2 -C1 -O1A { keep C2 in the alpha configuration} END PRESidue A26 {alpha(2,6) link for NANA} MODIfy ATOM +O6 TYPE=OA CHARge=-0.40 END MODIfy ATOM +C6 CHARge= 0.00 END DELEte ATOM +HO6 END MODIfy ATOM -C2 CHARge= 0.24 END DELEte ATOM -O2 END DELEte ATOM -HO2 END ADD BOND -C2 +O6 ADD ANGle +C6 +O6 -C2 ADD ANGle +O6 -C2 -C1 ADD ANGle +O6 -C2 -O6 ADD ANGle +O6 -C2 -C3 ADD DIHEdral +C6 +O6 -C2 -C1 ADD DIHEdral +C6 +O6 -C2 -O6 ADD DIHEdral +C6 +O6 -C2 -C3 ADD DIHEdral +O6 -C2 -C1 -O1A END set echo=true end