GLYCAM PARAMETERS (FOR AMBER 5.0, RESP 0.010), COPYRIGHT R.J.WOODS, CCRC 2000 MASS AC 12.01 0.00 CT ALPHA ANOMERIC CARBON (P94=PARM94) EC 12.01 0.00 CT BETA ANOMERIC CARBON OG 16.00 0.00 OS GLYCOSIDIC OXYGEN OL 16.00 0.00 OS RING OXYGEN FOR L- AND 1C4(D) SUGARS OH 16.00 0.00 OH HYDROXYL OXYGEN OS 16.00 0.00 OS RING OXYGEN SUGARS CL 35.45 0.00 Chlorine atom I2 40.08 0.00 CALCIUM ION (2+) BOND AC-CT 310.00 1.527 P94 K CT-CT EC-CT 310.00 1.519 P94 K CT-CT AC-H2 340.00 1.090 P94 CT-H2 EC-H2 340.00 1.090 P94 CT-H2 C -HC 331.00 1.090 P91 CT-HC FOR FORMYL GROUPS C -EC 317.00 1.570 P91 C-CT AB INITIO 6-31G* EC-N 337.00 1.460 P94 K CT-N AC-OS 320.00 1.416 AVG OF GAL MAN GLU L-ARA,K P94 CT-OS AC-OL 320.00 1.416 AVG OF GAL MAN GLU L-ARA,K P94 CT-OS EC-OS 320.00 1.425 AVG OF GAL GLU XYL,K P94 CT-OS EC-OL 320.00 1.425 AVG OF GAL GLU XYL,K P94 CT-OS CT-OL 320.00 1.410 P94 CT-OS AC-OG 320.00 1.405 AVG OF GAL MAN GLU L-ARA,K P94 CT-OS EC-OG 320.00 1.389 AVG OF GAL GLU XYL,K P94 CT-OS CT-OG 320.00 1.435 AVG OF MAN GLU GAL XYL,K P94 CT-OS AC-OH 320.00 1.396 AVG OF GAL MAN GLU L-ARA,K P94 CT-OS EC-OH 320.00 1.387 AVG OF GAL GLU XYL,K P94 CT-OS CT-CL 232.40 1.758 CT-CL for CH2CL2 from J.Phys.Chem.(1998)8070. CT-H2 340.0 1.100 CT-H2 for CH2CL2 from J.Phys.Chem.(1998)8070. ANGL AC-CT-CT 40.00 111.80 P94 K CT-CT-CT EC-CT-CT 40.00 109.40 P94 K CT-CT-CT CT-AC-CT 40.00 109.50 P94 CT-CT-CT CT-EC-CT 40.00 109.50 P94 CT-CT-CT AC-CT-H1 50.00 109.50 P94 CT-CT-H1 AC-CT-HC 50.00 109.50 P94 CT-CT-H1 EC-CT-H1 50.00 109.50 P94 CT-CT-H1 EC-CT-HC 50.00 109.50 P94 CT-CT-H1 EC-CT-N 80.00 109.70 P91 ALA JACS 94, 2657 AC-CT-N 80.00 109.70 P91 ALA JACS 94, 2657 AC-CT-OH 50.00 109.50 P94 CT-CT-OH EC-CT-OH 50.00 109.50 P94 CT-CT-OH EC-C -O2 70.00 117.00 P94 CT-C -O2 AC-CT-OS 50.00 109.50 P94 CT-CT-OS AC-CT-OL 50.00 109.50 P94 CT-CT-OS EC-CT-OS 50.00 109.50 P94 CT-CT-OS EC-CT-OL 50.00 109.50 P94 CT-CT-OS AC-CT-OG 50.00 109.50 P94 CT-CT-OS EC-CT-OG 50.00 109.50 P94 CT-CT-OS C -AC-CT 63.00 111.10 P94 C -CT-CT C -EC-CT 63.00 111.10 P94 C -CT-CT C -AC-OL 63.00 113.00 P94 K C -CT-N AB INITIO ANGLE C -EC-OL 63.00 113.00 P94 K C -CT-N AB INITIO ANGLE C -AC-OG 63.00 113.00 P94 K C -CT-N AB INITIO ANGLE C -EC-OG 63.00 113.00 P94 K C -CT-N AB INITIO ANGLE CT-CT-OL 50.00 109.50 P94 CT-CT-OS CT-CT-OG 50.00 109.50 P94 CT-CT-OS CT-AC-H2 50.00 109.50 P94 CT-CT-H2 CT-EC-H2 50.00 109.50 P94 CT-CT-H2 CT-EC-N 80.00 109.70 P91 CT-CT-N ALA JAAC 94, 2657 CT-AC-OG 50.00 109.50 P94 CT-CT-OS CT-EC-OG 50.00 109.50 P94 CT-CT-OS CT-AC-OH 50.00 109.50 P94 CT-CT-OS CT-EC-OH 50.00 109.50 P94 CT-CT-OS CT-AC-OS 50.00 110.50 P94 CT-CT-OS CT-AC-OL 50.00 110.50 P94 CT-CT-OS CT-EC-OS 50.00 109.50 P94 CT-CT-OS CT-EC-OL 50.00 109.50 P94 CT-CT-OS H2-EC-N 35.00 109.50 P91 H-CT-N H2-C -N 55.00 112.40 AVG K C-C=O, H-C-N FOR N-FORMYL H2-C -O 55.00 122.20 AVG K C-C=O, H-C-N FOR FORMYL H2-AC-OG 35.00 109.50 FROM FITTING TO DMM H2-EC-OG 35.00 109.50 FROM FITTING TO DMM H2-AC-OH 35.00 109.50 FROM FITTING TO DMM H2-EC-OH 35.00 109.50 FROM FITTING TO DMM H2-AC-OS 35.00 109.50 FROM FITTING TO DMM H2-AC-OL 35.00 109.50 FROM FITTING TO DMM H2-EC-OS 35.00 109.50 FROM FITTING TO DMM H2-EC-OL 35.00 109.50 FROM FITTING TO DMM H1-CT-OL 35.00 109.50 FROM FITTING TO DMM H1-CT-OG 35.00 109.50 FROM FITTING TO DMM C -N -EC 50.00 121.90 P94 C -N -CT EC-N -H 30.00 118.04 P94 CT-N -H AC-OS-CT 60.00 113.50 AVG OF GAL MAN GLU, K P94 CT-OS-CT AC-OL-CT 60.00 113.50 AVG OF GAL MAN GLU, K P94 CT-OS-CT EC-OS-CT 60.00 111.90 AVG OF GAL GLU XYL, K P94 CT-OS-CT EC-OL-CT 60.00 111.90 AVG OF GAL GLU XYL, K P94 CT-OS-CT AC-OG-CT 60.00 113.80 AVG OF GAL MAN GLU, K P94 CT-OS-CT EC-OG-CT 60.00 114.70 AVG OF GAL GLU XYL, K P94 CT-OS-CT N -EC-OS 106.90 107.90 AVE X'TAL ASN-GLCNAC, K FROM FAMM N -EC-OL 106.90 107.90 AVE X'TAL ASN-GLCNAC, K FROM FAMM OG-AC-OS 110.70 112.00 AVG OF GAL MAN GLU, K FROM DMM OG-AC-OL 110.70 112.00 AVG OF GAL MAN GLU, K FROM DMM OG-EC-OS 110.70 107.60 AVG OF GAL GLU XYL, K FROM DMM OG-EC-OL 110.70 107.60 AVG OF GAL GLU XYL, K FROM DMM OH-AC-OS 110.70 111.60 AVG OF GAL MAN GLU, K FROM DMM OH-AC-OL 110.70 111.60 AVG OF GAL MAN GLU, K FROM DMM OH-EC-OS 110.70 107.20 AVG OF GAL GLU XYL, K FROM DMM OH-EC-OL 110.70 107.20 AVG OF GAL GLU XYL, K FROM DMM AC-OH-HO 55.00 108.50 P94 CT-OH-HO EC-OH-HO 55.00 108.50 P94 CT-OH-HO OS-CT-C 63.00 112.36 (C -EC-OG) const., gaussian 94 angle (uronic H+) LCM O -C -EC 70.00 117.00 from (EC-C -O2) LCM OH-C -EC 70.00 117.00 from (EC-C -O2) LCM O2-C -OH 80.0 126.00 copied from parm96.dat ( AA GLU ) LCM CL-CT-CL 77.70 111.30 CT-CL for CH2CL2 from J.Phys.Chem.(1998)8070. CL-CT-H2 38.10 107.70 CT-CL for CH2CL2 from J.Phys.Chem.(1998)8070. DIHE X -CT-AC-X 9 1.40 0.00 3. P94 X-CT-CT-X X -CT-EC-X 9 1.40 0.00 3. P94 X-CT-CT-X X -CT-CT-X 9 1.40 0.00 3. P94 X-CT-CT-X X -CT-OG-X 3 1.15 0.00 3. P94 X-CT-OS-X X -AC-OS-X 3 1.15 0.00 3. P94 X-CT-OS-X X -AC-OL-X 3 1.15 0.00 3. P94 X-CT-OS-X X -EC-OS-X 3 1.15 0.00 3. P94 X-CT-OS-X X -EC-OL-X 3 1.15 0.00 3. P94 X-CT-OS-X X -CT-OS-X 3 1.15 0.00 3. P94 X-CT-OS-X X -CT-OL-X 3 1.15 0.00 3. P94 X-CT-OS-X X -C -N -X 4 10.00 180.00 2. P94 X-C-N-X X -N -CT-X 1 0.00 0.00 1. P94 X-N-CT-X H2-AC-OG-CT 1 0.00 0.00 3. EXO-ANOMERIC ALPHA H2-EC-OG-CT 1 0.00 0.00 3. EXO-ANOMERIC BETA C -EC-OG-CT 1 5.45 0.00 -1. EXO-ANOMERIC 1 0.47 0.00 -2. EFFECT ALPHA SIALIC ACID 1 -0.65 0.00 3. C-C-O-C AB INITIO CT-AC-OG-CT 1 0.00 0.00 3. EXO-ANOMERIC ALPHA CT-EC-OG-CT 1 0.00 0.00 3. EXO-ANOMERIC BETA CT-OG-AC-OS 1 1.39 265.77 -1. EXO-ANOMERIC 1 0.70 312.04 -2. EFFECT ALPHA 1 0.91 347.72 3. O-C-O-C CT-OG-AC-OL 1 1.39 94.64 -1. EXO-ANOMERIC 1 0.70 48.01 -2. EFFECT ALPHA (L and 1C4(D)) 1 0.91 12.07 3. O-C-O-C CT-OG-EC-OS 1 0.85 144.06 -1. EXO-ANOMERIC 1 0.74 353.55 -2. EFFECT BETA 1 0.97 6.43 3. O-C-O-C CT-OG-EC-OL 1 0.85 216.10 -1. EXO-ANOMERIC 1 0.74 6.72 -2. EFFECT (BETA 4C1(L) and ALPHA 1C4(D)) 1 0.97 353.73 3. O-C-O-C CT-CT-OG-AC 1 0.00 0. -3. (psi alpha=beta) 1 0.00 0. -2. (psi alpha=beta) 1 1.35 0. 1. (psi alpha=beta) H1-CT-OG-AC 1 0.00 0. 1. (psi alpha=beta) CT-CT-OG-EC 1 0.00 0. -3. (psi beta=alpha) 1 0.00 0. -2. (psi beta=alpha) 1 1.35 0. 1. (psi beta=alpha) H1-CT-OG-EC 1 0.00 0. 1. (psi beta=alpha) AC-CT-OG-AC 1 0.00 0. -3. (psi alpha=beta) 1 0.00 0. -2. (psi alpha=beta) 1 1.35 0. 1. (psi alpha=beta) AC-CT-OG-EC 1 0.00 0. -3. (psi alpha=beta) 1 0.00 0. -2. (psi alpha=beta) 1 1.35 0. 1. (psi alpha=beta) EC-CT-OG-AC 1 0.00 0. -3. (psi alpha=beta) 1 0.00 0. -2. (psi alpha=beta) 1 1.35 0. 1. (psi alpha=beta) EC-CT-OG-EC 1 0.00 0. -3. (psi alpha=beta) 1 0.00 0. -2. (psi alpha=beta) 1 1.35 0. 1. (psi alpha=beta) OS-EC-N -H 1 0.00 0.00 1. P91 X-N-CT-X OL-EC-N -H 1 0.00 0.00 1. P91 X-N-CT-X CT-EC-N -H 1 0.00 0.00 1. P91 X-N-CT-X H2-EC-N -H 1 0.00 0.00 1. P91 X-N-CT-X CT-EC-N -C 1 0.0 0.0 1. N-LINKED H2-EC-N -C 1 0.0 0.0 1. N-LINKED OS-EC-N -C 1 0.64 341.97 -1. N-LINKED 1 1.91 3.37 -2. GLYCOSIDE 1 -0.87 173.13 3. REVISED '97 OL-EC-N -C 1 0.64 18.03 -1. N-LINKED 1 1.91 356.63 -2. GLYCOSIDE (L and 2C4(D)) 1 -0.87 186.87 3. REVISED '97 C -N -CT-CT 1 0.50 180.0 -4. P94 2-N-Acetyl 1 0.15 180.0 -3. P94 CT-CT-N -C 1 0.00 0.00 -2. 1 0.53 0.0 1. P94 C -N -CT-AC 1 0.50 180.0 -4. P94 2-N-Acetyl 1 0.15 180.0 -3. P94 CT-CT-N -C 1 0.00 0.00 -2. 1 0.53 0.0 1. P94 C -N -CT-EC 1 0.50 180.0 -4. P94 2-N-Acetyl 1 0.15 180.0 -3. P94 CT-CT-N -C 1 0.00 0.00 -2. 1 0.53 0.0 1. P94 CT-EC-C -O2 1 0.00 0.00 2. AXIAL CO2- CT-EC-C -OH 1 0.00 0.00 2. copied from (CT-EC-C -O2) LCM OG-EC-C -O2 1 0.00 0.00 2. AXIAL CO2- OG-EC-C -OH 1 0.00 0.00 2. copied from (OG-EC-C -O2) LCM OL-EC-C -O2 2 2.80 180.00 2. AXIAL CO2- OL-EC-C -OH 2 2.80 180.00 2. copied from (OL-EC-C -O2) LCM CT-EC-C -O 1 0.00 0.00 2. copied from (CT-EC-C -O2) LCM OG-EC-C -O 1 0.00 0.00 2. copied from (OG-EC-C -O2) LCM OL-EC-C -O 2 2.80 180.00 2. copied from (OL-EC-C -O2) LCM OG-CT-CT-CT 1 -0.27 0.00 1. SCEE=1.0, SCNB=1.0 methylpropyl ether KNK OH-CT-CT-CT 1 -0.40 0.00 1. SCEE=1.0, SCNB=1.0 Propanol KNK OL-CT-CT-CT 1 -0.27 0.00 1. SCEE=1.0, SCNB=1.0 methylpropyl ether KNK OS-CT-CT-CT 1 -0.27 0.00 1. SCEE=1.0, SCNB=1.0 methylpropyl ether KNK OG-CT-CT-OH 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK 1 0.50 0.00 2. OH-CT-CT-OH 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK 1 0.50 0.00 2. An Approximate Parameter OG-CT-CT-OL 1 -0.87 0.00 1. SCEE=1.0, SCNB=1.0 6-O-methoxyglucose KNK OH-CT-CT-OL 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK 1 0.50 0.00 2. OG-CT-CT-OS 1 -0.87 0.00 1. SCEE=1.0, SCNB=1.0 6-O-methoxyglucose KNK OH-CT-CT-OS 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK 1 0.50 0.00 2. OS-CT-CT-OS 1 -0.87 0.00 1. SCEE=1.0, SCNB=1.0 6-O-methoxyglucose KNK OG-CT-AC-OH 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK 1 0.50 0.00 2. OH-CT-AC-OH 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK 1 0.50 0.00 2. An Approximate Parameter OG-CT-AC-OL 1 -0.87 0.00 1. SCEE=1.0, SCNB=1.0 6-O-methoxyglucose KNK OH-CT-AC-OL 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK 1 0.50 0.00 2. OG-CT-AC-OS 1 -0.87 0.00 1. SCEE=1.0, SCNB=1.0 6-O-methoxyglucose KNK OH-CT-AC-OS 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK 1 0.50 0.00 2. OG-CT-EC-OH 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK 1 0.50 0.00 2. OH-CT-EC-OH 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK 1 0.50 0.00 2. An Approximate Parameter OG-CT-EC-OL 1 -0.87 0.00 1. SCEE=1.0, SCNB=1.0 6-O-methoxyglucose KNK OH-CT-EC-OL 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK 1 0.50 0.00 2. OG-CT-EC-OS 1 -0.87 0.00 1. SCEE=1.0, SCNB=1.0 6-O-methoxyglucose KNK OH-CT-EC-OS 1 -0.67 0.00 -1. SCEE=1.0, SCNB=1.0 Glucose KNK 1 0.50 0.00 2. AC-CT-OH-HO 3 0.50 0.00 3. P94 X-CT-OH-X EC-CT-OH-HO 3 0.50 0.00 3. P94 X-CT-OH-X CT-AC-OH-HO 1 -0.90 0.00 -1. HO-OH-CT-CT Mannose 1 0.00 0.00 -2. 1 0.50 0.00 3. CT-EC-OH-HO 1 -0.90 0.00 -1. HO-OH-CT-CT Mannose 1 0.00 0.00 -2. 1 0.50 0.00 3. H2-AC-OH-HO 1 0.50 0.00 3. P94 X-CT-OH-X H2-EC-OH-HO 1 0.50 0.00 3. P94 X-CT-OH-X OS-AC-OH-HO 3 0.50 0.00 3. P94 X-CT-OH-X OL-AC-OH-HO 3 0.50 0.00 3. P94 X-CT-OH-X OS-EC-OH-HO 3 0.50 0.00 3. P94 X-CT-OH-X OL-EC-OH-HO 3 0.50 0.00 3. P94 X-CT-OH-X CT-CT-C -O2 1 0.00 0.00 -1. uronic H+ zero'd non-(Ox-xx-xx-Ox) LCM CT-CT-C -O2 1 0.00 0.00 -2. uronic H+ zero'd non-(Ox-xx-xx-Ox) LCM CT-CT-C -O2 1 0.00 0.00 3. uronic H+ zero'd non-(Ox-xx-xx-Ox) LCM H1-CT-C -O2 1 0.00 0.00 -1. uronic H+ zero'd non-(Ox-xx-xx-Ox) LCM H1-CT-C -O2 1 0.00 0.00 -2. uronic H+ zero'd non-(Ox-xx-xx-Ox) LCM H1-CT-C -O2 1 0.00 0.00 3. uronic H+ zero'd non-(Ox-xx-xx-Ox) LCM OS-CT-C -O2 2 0.00 0.00 -1. uronic H+ LCM OS-CT-C -O2 2 1.40 190.00 -2. uronic H+ LCM OS-CT-C -O2 2 0.09 160.00 -3. uronic H+ LCM OS-CT-C -O2 2 0.13 161.00 4. uronic H+ LCM IMPR X -X -N -H 5.25 180. 2. X -X -C -O 10.5 180. 2. X -O2-C -O2 10.5 180. 2. X -O2-C -OH 10.5 180. 2. HBON H OG 7557.00 2385.00 H OL 7557.00 2385.00 HW OG 7557.00 2385.00 HW OL 7557.00 2385.00 HO OG 7557.00 2385.00 HO OL 7557.00 2385.00 NONB AC 1.9080 0.0860 EC 1.9080 0.0860 I2 1.6000 0.1000 OG 1.8310 0.1400 OL 1.8310 0.1400 OS 1.8310 0.1400 CL 1.9480 0.2650 OH 1.7210 0.2104 OPLS (changed from old 2000a value June 2005 based on Xstal MD data S Wittkopp) END N.B. Correct rotational behavior for O-C-C-O fragments requires SCEE=SCNB=1.0. This is in contrast to "standard" AMBER, in which it is normal to set SCEE=1.2 and SCNB=2.0. Unless you are attempting to generate rotamer populations, it is OK to use the "standard" values. Using non-standard values (SCEE=SCNB=1.0) may be unacceptable when a protein is also present. GLYCAM contributors include: Karl N. Kirschner Laura C. Morris Sompathana Sundara