GLYCAM PARAMETERS (FOR AMBER 8.0, RESP 0.010), COPYRIGHT CCRC 2004 CG 12.01 ! sp3 C aliphatic CT 12.01 sp3 C aliphatic CY 12.01 sp3 C aliphatic - for sialic acid only! C 12.01 sp2 C carbonyl group H 1.008 H Bonded to nitrogen atoms H1 1.008 H aliph. bond. to C with 1 electrwd. groups H2 1.008 H aliph. bond. to C with 2 electrwd. groups HC 1.008 H aliph. bond. to C without electrwd. groups HO 1.008 H hydroxyl group HW 1.008 H TIP3P water N 14.01 sp2 N amide group O 16.00 O carbonyl group O2 16.00 O carboxyl group OH 16.00 O hydroxyl group OS 16.00 O ether OY 16.00 O ether - for sialic acid only! OW 16.00 O TIP3P water C H HO N NA NB NC N2 NT N2 N3 N* O OH OS P O2 OW-HW 553.0 0.9572 TIP3P water HW-HW 553.0 1.5136 TIP3P water CG-CG 310.0 1.520 Butane (gauche, and trans) CG-HC 360.0 1.095 Ethane CG-H1 410.0 1.092 Methanol CG-H2 440.0 1.105 1,1 Dimethoxyethane CG-OH 320.0 1.430 Methanol CG-C 220.0 1.530 2 Methylpropanoate CG-N 337.0 1.450 N-Methylethanamide C -O 999.0 1.220 N-Methylethanamide C -N 490.0 1.360 N-Methylethanamide C -O2 730.0 1.260 2 Methylpropanoate C -HC 331.0 1.090 Parm91 C -H1 410.0 1.092 Methanol OH-HO 700.0 0.960 Methanol N -H 600.0 1.010 N-Methylethanamide CG-OS 320.0 1.410 Parm94 CG-OY 320.0 1.410 Parm94 - for sialic acid only! CY-CG 310.0 1.520 Butane (gauche, and trans) - for sialic acid only! CY-OS 320.0 1.410 Parm94 - for sialic acid only! CY-OY 320.0 1.410 Parm94 - for sialic acid only! CY-C 220.0 1.530 2 Methylpropanoate - for sialic acid only! HW-OW-HW 100. 104.52 TIP3P water HW-HW-OW 0. 127.74 (found in crystallographic water with 3 bonds) HC-CG-HC 40.00 109.50 Methane, Ethane H1-CG-H1 45.00 109.50 Methanol, Propanol H2-CG-H2 45.00 109.50 Methanol, Propanol CG-CG-HC 45.00 112.60 Ethane CG-CG-H1 45.00 111.00 Propanol CG-CG-H2 45.00 111.00 Propanol CG-CG-CG 45.00 113.50 Propane OH-CG-CG 70.00 107.50 Ethanol H1-CG-OH 60.00 110.00 Methanol (best fit for trans and gauche hyrdogens) H2-CG-OH 60.00 110.00 Methanol (best fit for trans and gauche hyrdogens) CG-OH-HO 55.00 109.50 Methanol CG-OS-CG 50.00 108.50 Dimethylether CT-OS-CG 50.00 108.50 Dimethylether - for O-linking to proteins OS-CG-CG 70.00 108.50 Ethylmethyl ether OY-CG-CG 70.00 108.50 Ethylmethyl ether - for sialic acid only H1-CG-OS 60.00 110.00 Dimethyl ether (best fit for trans and gauche hyrdogens) H1-CG-OY 60.00 110.00 Dimethyl ether - for sialic acid only! H2-CG-OS 60.00 110.00 Dimethyl ether (best fit for trans and gauche hyrdogens) H1-C -O 60.00 110.00 Dimethyl ether (best fit for trans and gauche hyrdogens) H1-C -N 55.00 112.40 AVG K C-C=O, H-C-N FOR N-FORMYL - Approximate OS-CG-OS 100.00 112.00 Dimethylmethane, 1,1 Dimethoxyethane OH-CG-OS 100.00 112.00 Copy of OS-CG-OS (not derived) O2-C -O2 100.00 130.00 Acetate, 2-Methylpropanoate O2-C -CG 70.00 115.00 Aprroximate based from 2-Dimethylpropanoate and OH-CG-CG CG-C -N 70.00 115.60 Force constant taken from Parm94, Angle set to HF/6-31G(d) value N_Methylethanamide CG-C -O 80.00 121.70 Force constant taken from Parm94, Angle set to HF/6-31G(d) value N_Methylethanamide N -C -O 80.00 122.70 Force constant taken from Parm94, Angle set to HF/6-31G(d) value N_Methylethanamide N -CG-HC 50.00 110.10 Force constant taken from HC-CG-C Parm94, Angle set to average HF/6-31G(d) value N_Methylethanamide OS-CG-N 106.90 107.90 AVE X'TAL ASN-GLCNAC, K FROM FAMM (GLYCAM_93) CG-CG-N 80.00 109.70 Parm91 H1-CG-N 35.00 109.50 Parm91 H-CG-N H2-CG-N 35.00 109.50 Parm91 H-CG-N C -CG-CG 63.00 111.10 Parm94 C -CG-HC 50.00 109.50 Parm94 C -CG-H1 50.00 109.50 Parm94 C -CG-H2 50.00 109.50 Parm94 C -N -CG 50.00 120.00 Force constant taken from Parm94 - modified the angle by 2.9 degrees CG-N -CG 50.00 118.00 Parm94 H -N -CG 30.00 118.00 N-Methylethanamide C -N -H 60.00 122.00 Ethanamide H -N -H 30.00 119.00 Force constant taken from Parm94, Angle set to agree with C -N -H in ethanamide 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 OS-CG-C 63.00 112.36 Glycam_93 O2-C -OH 80.0 126.00 Parm96 OS-CY-CG 70.00 108.50 Ethylmethyl ether - for sialic acid only! OY-CY-CG 70.00 108.50 Ethylmethyl ether - for sialic acid only! OS-CY-C 63.00 112.36 Glycam_93 - for sialic acid only! OY-CY-C 63.00 112.36 Glycam_93 - for sialic acid only! OY-CY-OS 100.00 112.00 Dimethylmethane, 1,1 Dimethoxyethane - for sialic acid only! CG-CY-C 63.00 111.10 Parm94 - for sialic acid only! CG-OS-CY 50.00 108.50 Dimethylether - for sialic acid only! CG-OY-CY 50.00 108.50 Dimethylether - for sialic acid only! O2-C -CY 70.00 115.00 Aprroximate based from 2-Dimethylpropanoate and OH-CG-CG - for sialic acid only! HC-CG-CY 45.00 112.60 Ethane - for sialic acid only! CG-CG-CY 45.00 113.50 Propane - for sialic acid only! HC-CG-CG-HC 1 0.13 0.0 3. Ethane H1-CG-CG-HC 1 0.17 0.0 3. Ethanol, after H1-CG-CG-CG H2-CG-CG-HC 1 0.17 0.0 3. Ethanol, after H1-CG-CG-CG H1-CG-CG-H1 1 0.17 0.0 3. Ethanol H1-CG-CG-H2 1 0.17 0.0 3. Ethanol HC-CG-CG-CG 1 0.10 0.0 3. Propane H1-CG-CG-CG 1 0.15 0.0 3. 2-Dimethylbutanol H2-CG-CG-CG 1 0.15 0.0 3. 2-Dimethylbutanol HO-OH-CG-H1 1 0.18 0.0 3. Methanol HO-OH-CG-H2 1 0.18 0.0 3. Copy of HO-OH-CG-H1 (not derived) HO-OH-CG-CG 1 0.18 0.0 3. Ethanol, Isopropanol CG-CG-CG-CG 1 0.45 0.0 1. Butane OH-CG-CG-HC 1 0.05 0.0 3. Tertbutanol OH-CG-CG-H1 1 0.05 0.0 3. Tertbutanol OH-CG-CG-H2 1 0.05 0.0 3. Tertbutanol OH-CG-CG-CG 1 0.10 0.0 3. 2,3-Dimethylbutanol OS-CG-CG-CG 1 -0.27 0.0 1. Methylpropyl ether, Methyl 2-methylpropyl ether OY-CG-CG-CG 1 -0.27 0.0 1. Methylpropyl ether, - sialic acid only H1-CG-OS-CG 1 0.27 0.0 3. Dimethyl ether, Isobutyl methyl ether, etc H1-CT-OS-CG 1 0.27 0.0 3. Dimethyl ether, Isobutyl methyl ether, etc, O-linking to protein CG-OS-CG-CG 1 0.16 0.0 3. Ethyl methyl ether, Isopropyl methyl ether CT-OS-CG-CG 1 0.16 0.0 3. Ethyl methyl ether, Isopropyl methyl ether, O-linking to protein CG-OS-CT-CT 1 0.16 0.0 3. Ethyl methyl ether, Isopropyl methyl ether, O-linking to protein OH-CG-CG-OH 1 0.00 0.0 -1. 2,3-propanediol, 2-methyl-2,3-butanediol, etc 1 0.95 0.0 -2. 1 0.55 0.0 3. OH-CG-CG-OS 1 -1.10 0.0 -1. Ether-Alcohols 1 0.25 0.0 2. OH-CG-CG-OY 1 -1.10 0.0 -1. Ether-Alcohols - sialic acid only 1 0.25 0.0 2. H1-CG-CG-OY 1 0.05 0.0 3. Copy of H1-CG-CG-OS (not derived) OS-CG-CG-OS 1 0.82 0.0 2. DiEthers OS-CG-CG-OY 1 0.82 0.0 2. DiEthers - sialic acid only OS-CG-OH-HO 1 0.18 0.0 3. Copy of HO-OH-CG-CG (not derived) OS-CG-OS-CG 1 0.55 300.0 -1. 2,2-Dimethoxypropane 1 0.60 0.0 -2. 1 0.20 60.0 3. OS-CG-OS-CT 1 0.55 300.0 -1. 2,2-Dimethoxypropane, O-linking to protein 1 0.60 0.0 -2. 1 0.20 60.0 3. OH-CG-OS-CG 1 0.55 300.0 -1. Copy of OS-CG-OS-CG (not derived) 1 0.60 0.0 -2. 1 0.20 60.0 3. H2-CG-OS-CG 1 0.60 0.0 -2. Dimethoxymethane, after OS-CG-OS-CG 1 0.10 0.0 3. H2-CG-OS-CT 1 0.60 0.0 -2. Dimethoxymethane, after OS-CG-OS-CG, O-linking to protein 1 0.10 0.0 3. HC-CG-CG-OS 1 0.05 0.0 3. Ethyl methyl ether H1-CG-CG-OS 1 0.05 0.0 3. Ethyl methyl ether H2-CG-CG-OS 1 0.05 0.0 3. Ethyl methyl ether H -N -C -O 1 2.00 0.0 -1. Parm94 - Corrected to remove phase shift 1 -2.50 0.0 2. H -N -C -H1 1 -2.50 0.0 2. Parm94 - Corrected to remove phase shift H -N -C -CG 1 0.00 0.0 1. Ethanamide and N-Methylethanamide HC-CG-C -O 1 0.00 0.0 3. Ethanamide HC-CG-C -N 1 0.00 0.0 3. Ethanamide CG-OS-CG-N 1 -0.90 0.0 1. N-(2-Methoxyisopropyl)-ethanamide, N-(2-Methoxyethyl)-ethanamide OS-CG-CG-N 1 -1.30 0.0 1. N-(2-methoxyethyl)-ethanamide, N-(2-methyoxy-2-methyl-propyl)-ethanmide OY-CG-CG-N 1 -1.30 0.0 1. N-(2-methoxyethyl)-ethanamide - sialic acid only OS-CG-CG-H1 1 0.15 0.0 3. Parm94 OY-CG-CG-H1 1 0.15 0.0 3. Parm94 - sialic acid only OH-CG-CG-N 1 -1.50 0.0 1. N-(2-hydroxyethyl)-ethanamide, N-(2-Hydroxy-2-methyl-propyl)-ethanmide CG-CG-CG-N 1 0.40 0.0 1. N-(1,1,2,2-tetramethyl-propyl)-ethanamide, N-propyl-ethanamide HC-CG-CG-N 1 0.10 0.0 3. N-Isobutylethanamide H1-CG-CG-N 1 0.10 0.0 3. N-Isobutylethanamide H2-CG-CG-N 1 0.10 0.0 3. N-Isobutylethanamide N- CG-CG-N 1 0.00 0.0 1. N-(N-ethylethanamide)-ethanamide HC-CG-CG-C 1 0.10 0.0 3. Propane H1-CG-CG-C 1 0.10 0.0 3. Propane CG-CG-CG-C 1 0.45 0.0 3. Butane CG-CG-N -C 1 0.00 0.0 3. N-Isobutylethanamide, N-Isopropylethanamide OS-CG-N -C 1 0.00 0.0 3. Coupled to OS-CG-N-H OS-CG-N -H 1 0.00 0.0 3. Coupled to OS-CG-N-C CG-CG-N -H 1 0.10 0.0 3. N-Isobutylethanamide, N-Isopropylethanamide H1-CG-N -CG 1 0.00 0.0 3. N,N-Dimethylethanamide coupled to H1-CG-N-C H2-CG-N -CG 1 0.00 0.0 3. N,N-Dimethylethanamide coupled to H1-CG-N-C H1-CG-N -H 1 0.00 0.0 3. N-Isopropylethanamide Coupled to H1-CG-N-C H2-CG-N -H 1 0.00 0.0 3. N-Isopropylethanamide Coupled to H1-CG-N-C H1-CG-N -C 1 -0.17 0.0 3. N,N-Dimethylethanamide, N-Isopropylethanamide H2-CG-N -C 1 -0.17 0.0 3. N,N-Dimethylethanamide, N-Isopropylethanamide CG-N -C -O 1 -5.00 0.0 2. N-Methylethanamide, N-Isobutylethanamide CG-N -C -CG 1 0.00 0.0 2. N-Methylethanamide, N-Isobutylethanamide HC-CG-C -O2 2 0.00 0.0 1. Acetate CG-CG-C -O2 2 -1.50 0.0 2. Propanoate, 2-Methylpropanoate, 2-Dimethylpropanoate H1-CG-C -O2 2 0.00 0.0 1. 2-Methylpropanoate H2-CG-C -O2 2 0.00 0.0 1. 1_1_Dimethoxyacetate OS-CG-C -O2 2 -2.25 0.0 2. 2-Methoxy-2-methylpropanoate CG-OS-CG-C 1 0.00 0.0 -1. 1-Methoxy-1-Acetate THP, 1-Methoxy-1-Acetate THP Neutralized w/ Hbond 1 0.00 0.0 2. H1-CT-OS-CG 1 0.27 0.0 3. Protein Linkage: Dimethyl ether, Isobutyl methyl ether, etc CG-OS-CT-CT 1 0.16 0.0 3. Protein Linkage: Ethyl methyl ether, Isopropyl methyl ether CT-OS-CG-CG 1 0.16 0.0 3. Protein Linkage: Ethyl methyl ether, Isopropyl methyl ether OS-CG-OS-CT 1 0.55 300.0 -1. Protein Linkage: 2,2-Dimethoxypropane 1 0.60 0.0 -2. 1 0.20 0.0 3. CG-N -C -CT 1 0.00 0.0 2. Protein Linkage: N-Methylethanamide, N-Isobutylethanamide OY-CY-OS-CG 1 0.55 300.0 -1. 1-Methoxy-1-Acetate THP - for sialic acid only! 1 0.60 0.0 -2. 1 0.20 0.0 3. OS-CY-OY-CG 1 0.55 300.0 -1. 2,2-Dimethoxypropane - for sialic acid only! 1 0.60 0.0 -2. 1 0.20 60.0 3. OS-CY-CG-CG 1 -0.27 0.0 1. Methylpropyl ether, Methyl 2-methylpropyl ether - for sialic acid only! OY-CY-CG-CG 1 -0.27 0.0 1. Methylpropyl ether, Methyl 2-methylpropyl ether - for sialic acid only! OS-CY-CG-HC 1 0.05 0.0 3. Ethyl methyl ether - for sialic acid only! OY-CY-CG-HC 1 0.05 0.0 3. Ethyl methyl ether - for sialic acid only! CG-OS-CY-CG 1 0.16 0.0 3. Ethyl methyl ether, Isopropyl methyl ether - for sialic acid only! CG-OY-CY-CG 1 0.16 0.0 3. Ethyl methyl ether, Isopropyl methyl ether - for sialic acid only! OS-CY-C -O2 2 -2.25 0.0 2. 2-Methoxy-2-methylpropanoate - for sialic acid only! OY-CY-C -O2 2 -2.25 0.0 2. 2-Methoxy-2-methylpropanoate - for sialic acid only! CG-CY-C -O2 2 -1.50 0.0 2. Propanoate, 2-Methylpropanoate, 2-Dimethylpropanoate - for sialic acid only! CG-OS-CY-C 1 3.50 0.0 1. 1-Methoxy-1-Acetate THP, 1-Methoxy-1-Acetate THP Acid w/ Hbond - for sialic acid only! CG-OY-CY-C 1 0.00 0.0 1. 1-Methoxy-1-Acetate THP, 1-Methoxy-1-Acetate THP Acid w/ Hbond - for sialic acid only! HC-CG-CY-C 1 0.10 0.0 3. Propane - for sialic acid only! CG-CG-CY-C 1 0.45 0.0 3. Butane - for sialic acid only! CY-OS-CG-CG 1 0.16 0.0 3. Ethyl methyl ether, Isopropyl methyl ether - for sialic acid only! CY-OY-CG-CG 1 0.16 0.0 3. Ethyl methyl ether, Isopropyl methyl ether - for sialic acid only! CY-OS-CG-H1 1 0.27 0.0 3. Dimethyl ether, Isobutyl methyl ether, etc - for sialic acid only! CY-OY-CG-H1 1 0.27 0.0 3. Dimethyl ether, Isobutyl methyl ether, etc - for sialic acid only! CY-CG-CG-CG 1 0.45 0.0 1. Butane - for sialic acid only! CY-CG-CG-HC 1 0.10 0.0 3. Propane - for sialic acid only! CY-CG-CG-H1 1 0.15 0.0 3. 2-Dimethylbutanol - for sialic acid only! CY-CG-CG-OH 1 0.10 0.0 3. 2,3-Dimethylbutanol - for sialic acid only! X -X -N -H 1.0 180. 2. Parm94 X -X -C -O 10.5 180. 2. Parm94 X -X -N -CG 1.5 180. 2. X -X -N -H X -O2-C -O2 10.5 180. 2. Parm94 X -O2-C -OH 10.5 180. 2. X -O2-C -O2 HW OW 0000. 0000. 4. flag for fast water N NA N2 N* NC NB N3 NP NO C C* CA CB CC CN CM CK CQ CW CV CR CA CX CD MOD4 RE H 0.6000 0.0157 !Ferguson base pair geom. HO 0.0000 0.0000 OPLS Jorgensen, JACS,110,(1988),1657 HC 1.4870 0.0157 OPLS H1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963 H2 1.2870 0.0157 Veenstra et al JCC,8,(1992),963 HW 0.0000 0.0000 TIP3P water model O 1.6612 0.2100 OPLS O2 1.6612 0.2100 OPLS OW 1.7682 0.1521 TIP3P water model OH 1.7210 0.2104 OPLS OS 1.6837 0.1700 OPLS ether OY 1.6837 0.1700 OPLS ether - sialic acid only CG 1.9080 0.1094 Spellmeyer CY 1.9080 0.1094 Spellmeyer - sialic acid only C 1.9080 0.0860 OPLS N 1.8240 0.1700 OPLS END END Notes: This force field my be employed independently for simulating carbohydrtes or may be used in conjunction with Parm94 without introducing any conflict. 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. To obtain the current version of this force field and/or carbohydrate prep files go to the website http://www.glycam.ccrc.uga.edu. GLYCAM contributors include: Karl N. Kirschner, Sarah Tschampel, Austin Yongye, Robert Woods