GLYCAM PARAMETERS, COPYRIGHT R.J.WOODS, CCRC 2003 C 12.01 sp2 C carbonyl group Cg 12.01 Cg ALPHA ANOMERIC CARBON (P94=PARM94) Oh 16.00 Oh HYDROXYL OXYGEN O 16.00 carbonyl group oxygen Os 16.00 Os RING OXYGEN SUGARS OW 16.00 oxygen in TIP3P water O2 16.00 carboxyl and phosphate group oxygen Ng 14.01 sp2 nitrogen in amide groups H 1.008 H bonded to nitrogen atoms Hc 1.008 H aliph. bond. to C without electrwd.group H1 1.008 H aliph. bond. to C with 1 electrwd. group H2 1.008 H aliph. bond. to C with 2 electrwd.groups Ho 1.008 hydroxyl group HW 1.008 H in TIP3P water EP 0.000 lone pair C H Ho Ng NA NB NC N2 NT N2 N3 N* O Oh Os P O2 Cg-Cg 310.00 1.520 Butane (g, t) KNK Cg-Hc 360.00 1.095 Ethane KNK Cg-H1 410.00 1.092 Methanol KNK Cg-H2 440.00 1.105 1,1 Dimethoxyethane KNK Cg-Oh 320.00 1.430 Methanol KNK Cg-C 220.00 1.530 2 Methylpropanoate KNK Cg-Ng 337.00 1.450 N-Methylethanamide KNK C -O 999.00 1.220 N-Methylethanamide KNK C -Ng 490.00 1.360 N-Methylethanamide KNK C -O2 730.00 1.260 2 Methylpropanoate KNK C -Hc 331.00 1.090 P91 Cg-Hc FOR FORMYL GROUPS C -H1 410.00 1.092 Methanol KNK Oh-Ho 700.00 0.960 Methanol KNK Ng-H 600.00 1.010 N-Methylethanamide KNK Cg-CL 232.40 1.758 Cg-CL for CH2CL2 from J.Phys.Chem.(1998)8070. Cg-Os 320.0 1.410 Parm94 (JCC,7,(1986),230; NUCLEIC ACIDS) OW-HW 553.0 0.9572 TIP3P water HW-HW 553.0 1.5136 TIP3P water EP-Oh 553.0 0.7000 EP-Os 553.0 0.700 EP-O 553.0 0.450 Hc-Cg-Hc 40.00 109.50 Methane, Ethane KNK H1-Cg-H1 45.00 109.50 Methanol, Propanol KNK H2-Cg-H2 45.00 109.50 Methanol, Propanol KNK Cg-Cg-Hc 45.00 112.60 Ethane KNK Cg-Cg-H1 45.00 111.00 Propanol KNK Cg-Cg-H2 45.00 111.00 Propanol KNK Cg-Cg-Cg 45.00 113.50 Propane KNK Oh-Cg-Cg 70.00 107.50 Ethanol KNK H1-Cg-Oh 60.00 110.00 Methanol (best fit for trans and gauche hyrdogens) KNK H2-Cg-Oh 60.00 110.00 Methanol (best fit for trans and gauche hyrdogens) KNK Cg-Oh-Ho 55.00 109.50 Methanol KNK Cg-Os-Cg 50.00 108.50 Dimethylether KNK (108.5) Os-Cg-Cg 70.00 108.50 Ethylmethyl ether KNK (108.5) H1-Cg-Os 60.00 110.00 Dimethylether (best fit for trans and gauche hyrdogens) KNK H2-Cg-Os 60.00 110.00 Dimethylether (best fit for trans and gauche hyrdogens) KNK H1-C -O 60.00 110.00 Dimethylether (best fit for trans and gauche hyrdogens) KNK H1-C -Ng 55.00 112.40 AVG K C-C=O, H-C-NgFOR N-FORMYL - Approximate Os-Cg-Os 100.00 112.00 Dimethylmethane, 1,1 Dimethoxyethane KNK Oh-Cg-Os 100.00 112.00 Copy of Os-Cg-Os (not derived) JAH O2-C -O2 100.00 130.00 Acetate, 2-Methylpropanoate KNK O2-C -Cg 70.00 115.00 Aprroximate based from 2-Dimethylpropanoate and Oh-Cg-Cg KNK Cg-C -Ng 70.00 115.60 Force constant taken from Parm94, Angle set to HF/6-31G(d) value N_Methylethanamide KNK Cg-C -O 80.00 121.70 Force constant taken from Parm94, Angle set to HF/6-31G(d) value N_Methylethanamide KNK Ng-C -O 80.00 122.70 Force constant taken from Parm94, Angle set to HF/6-31G(d) value N_Methylethanamide KNK Ng-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 KNK Os-Cg-Ng 106.90 107.90 AVE X'TAL ASN-GLCNAC, K FROM FAMM (GLYCAM_93) * Cg-Cg-Ng 80.00 109.70 P91 Cg-Cg-Ng ALA JAAC 94, 2657 * H1-Cg-Ng 35.00 109.50 P91 H-Cg-Ng* H2-Cg-Ng 35.00 109.50 P91 H-Cg-Ng* 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 -Ng-Cg 50.00 120.00 Parm94 - modified the angle by 2.9 degrees KNK Cg-Ng-Cg 50.00 118.00 Parm94 H -Ng-Cg 30.00 118.00 N-Methylethanamide KNK C -Ng-H 60.00 122.00 Ethanamide KNK H -Ng-H 30.00 119.00 Force constant taken from Parm94, Angle set to agree with C -Ng-H in ethanamide KNK H2-C -Ng 55.00 112.40 AVG K C-C=O, H-C-NgFOR N-FORMYL H2-C -O 55.00 122.20 AVG K C-C=O, H-C-NgFOR FORMYL Os-Cg-C 63.00 112.36 (C -EC-OG) const., gaussian 94 angle (uronic H+) LCM O2-C -Oh 80.0 126.00 copied from parm96.dat ( AA GLU ) LCM CL-Cg-CL 77.70 111.30 Cg-CL for CH2CL2 from J.Phys.Chem.(1998)8070. CL-Cg-H2 38.10 107.70 Cg-CL for CH2CL2 from J.Phys.Chem.(1998)8070. HW-OW-HW 100. 104.52 TIP3P water HW-HW-OW 0. 127.74 (found in crystallographic water with 3 bonds) Hc-Cg-Cg-Hc 9 1.20 0.00 3. SCEE=1.0 SCNB=1.0 Ethane Hs=0 charge KNK H1-Cg-Cg-Hc 1 0.17 0.00 3. SCEE=1.0 SCNB=1.0 Ethanol, after H1-Cg-Cg-Cg KNK H2-Cg-Cg-Hc 1 0.17 0.00 3. SCEE=1.0 SCNB=1.0 Ethanol, after H1-Cg-Cg-Cg KNK H1-Cg-Cg-H1 1 0.17 0.00 3. SCEE=1.0 SCNB=1.0 Ethanol Hs=0 charge KNK H1-Cg-Cg-H2 1 0.17 0.00 3. SCEE=1.0 SCNB=1.0 Ethanol Hs=0 charge KNK Hc-Cg-Cg-Cg 9 0.90 0.00 3. SCEE=1.0 SCNB=1.0 Propane Hs=0 charge KNK H1-Cg-Cg-Cg 6 0.90 0.00 3. SCEE=1.0 SCNB=1.0 2-Dimethylbutanol Hs=0 charge KNK H2-Cg-Cg-Cg 6 0.90 0.00 3. SCEE=1.0 SCNB=1.0 2-Dimethylbutanol Hs=0 charge KNK Ho-Oh-Cg-H1 1 0.18 0.00 3. SCEE=1.0 SCNB=1.0 Methanol Hs=0 charge KNK Ho-Oh-Cg-H2 1 0.18 0.00 3. SCEE=1.0 SCNB=1.0 Copy of Ho-Oh-Cg-H1 (not derived) JAH Ho-Oh-Cg-Cg 1 0.18 0.00 3. SCEE=1.0 SCNB=1.0 Ethanol, isopropanol Hs=0 charge KNK Ho-Oh-Cg-Os 1 0.18 0.00 3. SCEE=1.0 SCNB=1.0 Copy of Ho-Oh-Cg-Cg (not derived) JAH Cg-Cg-Cg-Cg 1 0.45 0.00 1. SCEE=1.0 SCNB=1.0 Butane Hs=0 charge KNK Oh-Cg-Cg-Hc 1 0.05 0.00 3. SCEE=1.0 SCNB=1.0 Tertbutanol Hs=0 charge KNK Oh-Cg-Cg-H1 1 0.05 0.00 3. SCEE=1.0 SCNB=1.0 Tertbutanol Hs=0 charge KNK Oh-Cg-Cg-H2 1 0.05 0.00 3. SCEE=1.0 SCNB=1.0 Tertbutanol Hs=0 charge KNK Oh-Cg-Cg-Cg 3 0.30 0.00 3. SCEE=1.0 SCNB=1.0 2,3-Dimethylbutanol Hs=0 KNK Os-Cg-Cg-Cg 1 -0.27 0.00 1. SCEE=1.0 SCNB=1.0 Methylpropyl Ether, Methyl 2methylpropylether KNK H1-Cg-Os-Cg 3 0.80 0.00 3. SCEE=1.0 SCNB=1.0 Dimethyl Ether,Isobutyl Methyl Ether, etc KNK Cg-Os-Cg-Cg 1 0.16 0.00 3. SCEE=1.0 SCNB=1.0 Ethyl Methyl Ether, Isopropyl Methyl Ether KNK Oh-Cg-Cg-Oh 1 -1.00 0.00 -1. SCEE=1.0 SCNB=1.0 2,3-propanediol, 2-methyl 2,3-butanediol, etc KNK 1 0.95 0.00 -2. SCEE=1.0 SCNB=1.0 1 0.55 0.00 3. SCEE=1.0 SCNB=1.0 Oh-Cg-Cg-Os 1 -1.10 0.00 -1. SCEE=1.0 SCNB=1.0 Ether-Alcohols KNK 1 0.25 0.00 -2. SCEE=1.0 SCNB=1.0 1 0.00 0.00 3. SCEE=1.0 SCNB=1.0 Os-Cg-Cg-Os 1 0.82 0.00 2. SCEE=1.0 SCNB=1.0 DiEthers KNK Os-Cg-Os-Cg 1 0.55 300.00 -1. SCEE=1.0 SCNB=1.0 2,2-Dimethoxypropane KNK 1 0.60 0.00 -2. SCEE=1.0 SCNB=1.0 1 0.20 60.00 3. SCEE=1.0 SCNB=1.0 Oh-Cg-Os-Cg 1 0.55 300.00 -1. SCEE=1.0 SCNB=1.0 Copy of Os-Cg-Os-Cg (not derived) JAH 1 0.60 0.00 -2. SCEE=1.0 SCNB=1.0 1 0.20 60.00 3. SCEE=1.0 SCNB=1.0 H2-Cg-Os-Cg 1 0.00 0.00 -1. SCEE=1.0 SCNB=1.0 Dimethoxymethane, after Os-Cg-Os-Cg KNK 1 0.60 0.00 -2. SCEE=1.0 SCNB=1.0 1 0.20 0.00 3. SCEE=1.0 SCNB=1.0 Hc-Cg-Cg-Os 1 0.05 0.00 3. SCEE=1.0 SCNB=1.0 Ethyl Methyl ether KNK H -Ng-C -O 1 2.00 0.00 -1. SCEE=1.0 SCNB=1.0 ff99SB protein backbone JAH 1 -2.50 0.00 2. SCEE=1.0 SCNB=1.0 Coupled with H -Ng-C -Cg Ethanamide plus Cg-N-C-O N-Methylthanamide KNK H -Ng-C -H1 4 -10.00 0.00 2. SCEE=1.0 SCNB=1.0 Parm94 - Corrected to remove phase shift H -Ng-C -Cg 1 0.00 0.00 1. SCEE=1.0 SCNB=1.0 Coupled with H -Ng-C -O Ethanamide and N-Methylthanamide KNK Hc-Cg-C -O 1 0.00 0.00 3. SCEE=1.0 SCNB=1.0 Ethanamide KNK Hc-Cg-C -Ng 1 0.00 0.00 3. SCEE=1.0 SCNB=1.0 Ethanamide KNK Cg-Os-Cg-Ng 1 -0.90 0.00 1. SCEE=1.0 SCNB=1.0 Methoxy-N-Isopropylethanamide, Methoxy-N-Ethylethanamide KNK Os-Cg-Cg-Ng 1 0.00 0.00 2. SCEE=1.0 SCNB=1.0 KNK Os-Cg-Cg-Os V2=0.82 ????? Os-Cg-Cg-H1 9 1.40 0.00 3. SCEE=1.0 SCNB=1.0 Parm94 X-Cg-Cg-X term - should I make it from Hc-Cg-Cg-Os ?? Os-Cg-Cg-H2 9 1.40 0.00 3. SCEE=1.0 SCNB=1.0 Parm94 X-Cg-Cg-X term - should I make it from Hc-Cg-Cg-Os ?? Oh-Cg-Cg-Ng 1 0.00 0.00 2. SCEE=1.0 SCNB=1.0 KNK Os-Cg-Cg-Os V2=0.82 ????? Cg-Cg-Cg-Ng 1 0.00 0.00 2. SCEE=1.0 SCNB=1.0 KNK ?? Hc-Cg-Cg-Ng 1 0.10 0.00 3. SCEE=1.0 SCNB=1.0 N-Isobutylethanamide KNK H1-Cg-Cg-Ng 1 0.10 0.00 3. SCEE=1.0 SCNB=1.0 N-Isobutylethanamide KNK H2-Cg-Cg-Ng 1 0.10 0.00 3. SCEE=1.0 SCNB=1.0 N-Isobutylethanamide KNK Hc-Cg-Cg-C 9 0.90 0.00 3. SCEE=1.0 SCNB=1.0 Propane Hs=0 charge KNK ?? Cg-Cg-Ng-C 1 0.00 0.00 3. SCEE=1.0 SCNB=1.0 N-Isobutylethanamide, N-Isopropylethanamide KNK Coupled to Cg-Cg-N-H, H1-Cg-N-C Os-Cg-Ng-C 1 0.00 0.00 3. SCEE=1.0 SCNB=1.0 KNK Coupled to Os-Cg-N-H Os-Cg-Ng-H 1 0.00 0.00 3. SCEE=1.0 SCNB=1.0 KNK Coupled to Os-Cg-N-C Cg-Cg-Ng-H 1 0.00 0.00 3. SCEE=1.0 SCNB=1.0 N-Isobutylethanamide, N-Isopropylethanamide KNK Coupled to Cg-Cg-N-C H1-Cg-Ng-Cg 1 0.00 0.00 3. SCEE=1.0 SCNB=1.0 N,N-Dimethylethanamide coupled to H1-Cg-N-C KNK H2-Cg-Ng-Cg 1 0.00 0.00 3. SCEE=1.0 SCNB=1.0 N,N-Dimethylethanamide coupled to H1-Cg-N-C KNK H1-Cg-Ng-H 1 0.00 0.00 3. SCEE=1.0 SCNB=1.0 N-Isopropylethanamide Coupled to H1-Cg-N-C KNK H2-Cg-Ng-H 1 0.00 0.00 3. SCEE=1.0 SCNB=1.0 N-Isopropylethanamide Coupled to H1-Cg-N-C KNK H1-Cg-Ng-C 1 -0.17 0.00 3. SCEE=1.0 SCNB=1.0 N,N-Dimethylethanamide, N-Isopropylethanamide KNK H2-Cg-Ng-C 1 -0.17 0.00 3. SCEE=1.0 SCNB=1.0 N,N-Dimethylethanamide, N-Isopropylethanamide KNK Cg-Ng-C -O 1 -5.00 0.00 2. SCEE=1.0 SCNB=1.0 N-Methylethanamide, N-Isobutylethanamide coupled to Cg-N-C-Cg KNK Cg-Ng-C -Cg 1 0.00 0.00 2. SCEE=1.0 SCNB=1.0 N-Methylethanamide, N-Isobutylethanamide coupled to Cg-N-C-O KNK Hc-Cg-C -O2 2 0.00 0.00 1. SCEE=1.0 SCNB=1.0 Acetate KNK Cg-Cg-C -O2 2 -1.50 0.00 2. SCEE=1.0 SCNB=1.0 Propanoate, 2-Methylpropanoate, 2-Dimethylpropanoate KNK H1-Cg-C -O2 2 0.00 0.00 1. SCEE=1.0 SCNB=1.0 2-Methylpropanoate KNK H2-Cg-C -O2 2 0.00 0.00 1. SCEE=1.0 SCNB=1.0 1_1_Dimethoxyacetate KNK Os-Cg-C -O2 2 0.00 0.00 1. SCEE=1.0 SCNB=1.0 Cg-Os-Cg-C 1 0.80 0.00 2. SCEE=1.0 SCNB=1.0 2-Methylpropanoate, 2-Methoxy-2-Methylpropanoate KNK X -X -Ng-H 1.00 180. 2. SCEE=1.0 SCNB=1.0 X -X -C -O 10.5 180. 2. SCEE=1.0 SCNB=1.0 X -X -Ng-Cg 10.5 180. 2. SCEE=1.0 SCNB=1.0 X -O2-C -O2 10.5 180. 2. SCEE=1.0 SCNB=1.0 X -O2-C -Oh 10.5 180. 2. SCEE=1.0 SCNB=1.0 HW OW 0000. 0000. 4. flag for fast water Ng NA N2 N* NC NB N3 NP NO C C* CA CB CC CN CM CK CQ CW CV CR CA CX CY 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 1.7683 0.1520 TIP3P water model Oh 1.7210 0.2104 OPLS Os 1.6837 0.1700 OPLS ether Cg 1.9080 0.1094 Spellmeyer C 1.9080 0.0860 OPLS Ng 1.8240 0.1700 OPLS EP 1.0000 0.0000 lone pair END END