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Force field parameters 54A7 Tables 2.4.1 2.5.2.1 2.5.3.1 2.5.4.1 2.5.5.1.1 2.5.6.2.1 2.5.6.2.2 2.5.6.2.3 2.5.6.2.4 2.5.6.2.5 2.5.6.3.1 2.5.6.5.1 2.5.6.5.2 2.5.6.5.3 2.5.6.5.4 2.5.6.5.5 4.2.1 4.2.2 4.2.3 Mass atom type codes, masses and names Bond stretching parameters Bond-angle bending parameters Improper (harmonic) dihedral angle parameters (Trigonometric) dihedral torsional angle parameters Non-bonded atom types and integer atom codes Normal van der Waals parameters (Vacuo) normal van der Waals parameters Selection of van der Waals (repulsive) C12½ (I,I) parameters Normal van der Waals parameters for mixed atom type pairs (I,J) Third-neighbour van der Waals parameters Atomic charges and charge group definitions for amino acid residues Atomic charges for various (co)solvents Atomic charges and charge group definitions for nucleotides Atomic charges and charge group definitions for lipids Atomic charges and charge group definitions for carbohydrates 54A7 Solute building blocks 54A7 Solvent building blocks 54A7 End group building blocks Changes with respect to 53A6 in bold Torsional angle energy terms for the polypeptide and dihedral angles are changed The choice of the C12 parameter for the interaction between O(IAC=1) and N(IAC=6) A new van der Waals nonbonded atom type for a charged CH3 group is added (IAC=54) The van der Waals parameters for the Na+(IAC=37) and CL-(IAC=38) are modified [A578] Two extra improper dihedral angle terms have been added to facilitate free energy calculations 1 Table 2.4.1 GROMOS mass atom type codes, masses and names mass atom type code N 1 3 4 5 6 12 14 16 19 23 24 28 31 32 35 39 40 56 63 65 80 mass in a.m.u. ATMAS[N] 1.008 13.019 14.027 15.035 16.043 12.011 14.0067 15.9994 18.9984 22.9898 24.305 28.08 30.9738 32.06 35.453 39.948 40.08 55.847 63.546 65.37 79.904 mass atom name ATMASN[N] H CH1 CH2 CH3 CH4 C N O F NA MG SI P S CL AR CA FE CU ZN BR 2 Table 2.5.2.1 GROMOS bond-stretching parameters Bond-type code Force constant Ideal bond length K bn b0n K bharm n nm B0[N] kcalmol-1Å-2 harm = K bn ICBH[N] ICB[N] 1 2 3 4 5 6 7 8 9 10 Examples of usage in terms of nonbonded atom types / 2b02n 106kJmol-1nm-4 CB[N] 15.7 18.7 12.3 37.0 16.6 13.4 12.0 8.87 10.6 11.8 0.100 0.100 0.109 0.112 0.123 0.125 0.132 0.133 0.133 0.133 11 12 13 14 15 16 10.5 11.7 10.2 11.0 8.66 10.8 0.134 0.134 0.136 0.138 0.139 0.139 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 8.54 8.18 9.21 6.10 8.71 5.73 7.64 8.60 8.37 5.43 7.15 4.84 4.72 2.72 5.94 5.62 3.59 0.140 0.143 0.143 0.1435 0.147 0.148 0.148 0.148 0.150 0.152 0.153 0.161 0.163 0.178 0.178 0.183 0.187 3 H – OA H – N (all) HC – C C – O (CO bound to heme) C –O C – OM CR1 – NR (6-ring) H – S C – NT, NL C, CR1 – N, NR, CR1, C (peptide, 5-ring) C – N, NZ, NE C – NR (no H) (6-ring) C – OA, FTfe – CTfe C – NR (heme) CH2 – C, CR1 (6-ring) C, CR1 – CH2, C, CR1 (6–ring) C, CR1, CH2 – NR (6-ring) CHn – OA CHn – OM CHn – OA (sugar) CHn – N, NT, NL, NZ, NE CHn – NR (5-ring) CHn – NR (6-ring) O, OM – P O – S CHn – CHn (sugar) C, CHn – C, CHn OA – P OA – SI FE – C (CO bound to heme) CH3 – S CH2 – S CH1 – SI 750 895 700 2220 1200 1000 1000 750 900 1000 900 1000 900 1000 800 1000 800 800 900 600 900 600 800 900 900 600 800 600 600 412 900 900 600 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 0.640 0.628 5.03 0.540 23.2 12.1 8.12 8.04 4.95 8.10 13.1 10.3 8.71 2.68 2.98 2.39 2.19 3.97 3.04 0.198 0.200 0.204 0.221 0.100 0.110 0.1758 0.153 0.193799 0.176 0.1265 0.135 0.163299 0.233839 0.290283 0.279388 0.291189 0.2077 0.287407 4 NR (His) – FE (43A1) NR (heme) – FE S – S NR (His) – FE HWat – OWat HChl – CChl CChl – CLChl ODmso – SDmso SDmso – CDmso CCl4 – CLCl4 CUrea – OUrea CUrea – NUrea HWat – HWat HChl – CLChl CLChl – CLChl ODmso – CDmso CDmso – CDmso HMet – CMet CLCl4 – CLCl4 120 120 1000 126 1110 700 1200 900 890 1200 1000 900 1110 700 1200 890 890 820 1200 Table 2.5.3.1 GROMOS bond-angle bending parameters Bond-angle type code Force constant Ideal bond angle 0 Kn g ( K harm ICTH[N] ICT[N] 1 n Example of usage in terms of nonbonded atom types Kharm n n , n , Ek T ) kJmol-1 CT[N] 0 B kcalmol-1rad-2 degree (T0[N]) 380 90.0 2 420 90.0 3 4 5 6 7 8 405 475 420 490 465 285 96.0 100.0 103.0 104.0 108.0 109.5 9 320 109.5 10 380 109.5 11 425 109.5 12 13 450 520 109.5 109.5 14 15 450 530 109.6 111.0 16 17 18 19 20 21 22 23 24 25 545 50.0 460 610 465 620 635 390 445 505 113.0 115.0 115.0 115.0 116.0 116.0 117.0 120.0 120.0 120.0 26 27 28 530 560 670 120.0 120.0 120.0 5 NR (heme) – FE – C (CO bound to heme) NR(heme) – FE – NR(heme), NR (His) H – S – CH2 CH2 – S – CH3 OA – P – OA CH2 – S – S NR, C, CR1(5–ring) CHn – CHn – CHn, NR(6-ring) (sugar) CHn, OA – CHn – OA, NR(ring) (sugar) H – NL, NT – H, CHn – OA – CHn(sugar) H – NL – C, CHn H – NT – CHn X – OA, SI – X CH ,C – CHn – C, CHn, OA,OM, N, NE OM – P – OA CHn – CHn – C, CHn, OA, NR, NT, NL CHn – CH2 – S NR(heme) – FE – NR (His) (43A1) H – N – CHn CHn, C – C – OA, N, NT, NL H – NE – CH2 CH2 – N – CH1 CH3 – N – C, CHn – C – OM H – NT, NZ, NE – C H – NT, NZ – H H – N – CH3, H, HC – 6-ring, H –NT – CHn P, SI – OA – CHn, P N, C, CR1 (6-ring, no H) NZ – C – NZ, NE 90 100 95 110 95 110 100 60 68 80 90 95 110 95 110 110 10 90 120 90 120 120 70 80 90 95 100 120 29 30 780 685 120.0 121.0 31 32 33 700 415 730 122.0 123.0 124.0 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 375 750 575 640 770 760 2215 91350 434 484 632 469 503 443 618 507 448 524 531 636 690 125.0 125.0 126.0 126.0 126.0 132.0 155.0 180.0 109.5 107.57 111.30 97.4 106.75 108.53 109.5 107.6 109.5 110.3 111.4 117.2 121.4 6 OM – P – OM O – C – CHn, C CH3 – N – CHn CH1, CH2 – N – C H –N –C O – C – OA, N, NT, NL C – NE – CH2 FE – NR – CR1 (5-ring) – H, HC – 5-ring X(noH) – 5-ring OM – C – OM 5, 6 ring connnection SI – OA – SI Fe – C – O (CO bound to heme) HWat – OWat – HWat HChl – CChl – CLChl CLChl – CChl – CLChl CDmso – SDmso – CDmso CDmso – SDmso – ODmso HMet – OMet – CMet CLCl4 – CCl4 – CLCl4 FTfe – CTfe – FTfe HTfe – OTfe – CHTfe OTfe – CHTfe – CTfe CHTfe – CTfe – FTfe NUrea – CUrea – NUrea OUrea – CUrea – NUrea 140 120 120 70 120 60 120 90 100 120 100 95 57 92 105 131 110 110 95 131 110 95 110 110 120 120 Table 2.5.4.1 GROMOS improper (harmonic) dihedral angle parameters Improper dihedral-angle type code ICQH[N] ICQ[N] 1 2 3 4 5 Force constant Ideal improper dihedral angle K n 0 kJmol-1 degree-2 CQ[N] degree (Q0[N]) Example of usage K n n kcalmol-1 rad-2 0.0510 0.102 0.0 35.26439 0.204 0.0510 0.102 0.0 180.0 -35.26439 7 planar groups tetrahedral centres heme iron planar groups tetrahedral centres 40 80 160 40 80 Table 2.5.5.1 GROMOS (trigonometric) dihedral torsional angle parameters Dihedralangle type code ICPH[N] ICP[N] 1 Force constant Phase shift Multiplici ty Kn cos(δn) mn kJmol-1 CP[N] Example of usage in terms of nonbonded atom types K n kcalmol-1 PD[N] NP[N] 2.67 -1.0 1 2 3.41 -1.0 1 3 4.97 -1.0 1 4 5.86 -1.0 1 5 9.35 -1.0 1 6 9.45 -1.0 1 7 8 9 2.79 5.35 1.53 +1.0 +1.0 -1.0 1 1 2 10 11 12 13 5.86 7.11 16.7 24.0 -1.0 -1.0 -1.0 -1.0 2 2 2 2 14 15 16 17 18 19 20 33.5 41.8 0.0 0.418 2.09 3.14 5.09 -1.0 -1.0 +1.0 +1.0 +1.0 +1.0 +1.0 2 2 2 2 2 2 2 21 22 23 24 16.7 1.05 1.26 1.30 +1.0 +1.0 +1.0 +1.0 2 3 3 3 25 2.53 +1.0 3 CHn – CHn – CHn – OA (sugar) C4 – C5 – C6 – O6 a OA – CHn – OA – CHn, H ( sugar) O5 – C1 – O1 – C1’,H1 OA – CHn – CHn – OA (sugar) C4 – C5 – C6 – O6 a N – CHn – CHn – OA (lipid) OA – CHn – CHn – OA (sugar) O5 – C5 – C6 – O6 b OA – CHn – OA – CHn, H ( sugar) O5 – C1 – O1 – C1’,H1 P – O5* – C5* – C4* (dna) O5* – C5* – C4* – O4* (dna) C1 – C2 – CAB – CBB (heme) –C–C– –C–OA– (at ring) –C–OA– (carboxyl) CHn – OA – C – CHn (ester lipid) –C–N, NT, NE, NZ,NR– –C–CR1– (6-ring) –CH1 (sugar)–NR(base)– O–CH1–CHn–no O O–CH1–CHn–O –OA–P– CHn – O – P – O (dna, phosphodiester) –S–S– –OA–P– –CHn–OA(no sugar)– HTfe – OTfe – CHTfe – CTfe O5* – C5* – C4* – O4* (dna) 8 0.6 0.8 1.2 1.4 2.2 2.3 0.7 1.3 0.4 1.4 1.7 4.0 5.7 8.0 10.0 0.0 0.1 0.5 0.75 1.2 4.0 0.25 0.3 0.3 0.6 26 27 2.93 3.19 +1.0 +1.0 3 3 28 3.65 +1.0 3 29 3.77 +1.0 3 30 3.90 +1.0 3 31 32 4.18 4.69 +1.0 +1.0 3 3 33 34 35 5.44 5.92 7.69 +1.0 +1.0 +1.0 3 3 3 36 8.62 +1.0 3 37 9.50 +1.0 3 38 39 40 41 42 43 44 45 0.0 1.0 1.0 3.77 3.50 2.80 0.70 0.40 +1.0 -1.0 +1.0 +1.0 -1.0 +1.0 -1.0 +1.0 4 6 6 6 2 3 6 6 –CH2–S– CHn – O – P – O (dna, phosphodiester) OA – CHn – OA – CHn, H ( sugar) O5 – C1 – O1 – C1’,H1 –C,CHn,SI– NT,NL,OA(sugar)– CHn – CHn – OA – H (sugar) HC–C–S– OA – CHn – OA – CHn, H ( sugar) O5 – C1 – O1 – C1’,H1 HC–C–C– –CHn,SI–CHn– OA – CHn – CHn – OA (sugar) C4 – C5 – C6 – O6 a N – CHn – CHn – OA (lipid) OA – CHn – CHn – OA (sugar) O5 – C5 – C6 – O6 b –NR–FE– –CHn–N,NE– –CHn–C,NR (ring), CR1– –CHn–NT– –CHn–C– –CHn–N– –CHn–N– –CHn–C– 0.7 0.8 0.9 0.9 0.9 1.0 1.1 1.3 1.4 1.8 2.1 2.3 0.0 0.24 0.24 0.9 0.84 0.67 0.17 0.10 a) To be used if – C5 – C6 – O6 and adjacent – C4 – O4 – are axial and the other equatorial, as in galactose b) To be used if – C5 – C6 – O6 and adjacent – Cn – On – Hn are both simultaneously axial or equatorial, as in glucose 9 Table 2.5.6.2.1 GROMOS 54A7/54B7 non-bonded atom types and integer atom codes integer atom code IAC[N] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 atom type TYPE[N] O OM OA OE OW N NT NL NR NZ NE C CH0 CH1 CH2 CH3 CH4 CH2r CR1 HC H DUM S CU1+ CU2+ FE ZN2+ MG2+ CA2+ P, SI AR F CL BR CMet OMet NA+ CLCChl CLChl HChl SDmso description carbonyl oxygen (C=O) carboxyl oxygen (CO-) hydroxyl or sugar oxygen ether or ester oxygen water oxygen peptide nitrogen (NH) terminal nitrogen (NH2) terminal nitrogen (NH3) aromatic nitrogen Arg NH (NH2) Arg NE (NH) bare carbon bare sp3 carbon, 4 bound heavy atoms aliphatic or sugar CH-group aliphatic or sugar CH2-group aliphatic CH3-group methane CH2-group in a ring aromatic CH-group hydrogen bound to carbon hydrogen not bound to carbon dummy atom sulphur copper (charge 1+) copper (charge 2+) iron (heme) zinc (charge 2+) magnesium (charge 2+) calcium (charge 2+) phosphor or silicon argon fluor (non-ionic) chlorine (non-ionic) bromine (non-ionic) CH3-group in methanol (solvent) oxygen in methanol (solvent) sodium (charge 1+) chloride (charge 1-) carbon in chloroform (solvent) chloride in chloroform (solvent) hydrogen in chloroform (solvent) sulphur in DMSO (solvent) 10 43 44 45 46 47 48 49 50 51 52 53 54 CDmso ODmso CCl4 CLCl4 FTfe CTfe CHTfe OTfe CUrea OUrea NUrea CH3p CH3-group in DMSO (solvent) oxygen in DMSO (solvent) carbon in carbontetrachloride (solvent) chloride in carbontetrachloride (solvent) fluor in trifluoroethanol carbon in trifluoroethanol CH2-group in trifluoroethanol oxygen in trifluoroethanol carbon in urea oxygen in urea nitrogen in urea positively charged methyl 11 Table 2.5.6.2.2 GROMOS 54A7 normal van der Waals parameters integer atom code atom type (C12(I,I))½ (C6(I,I))½ [kJmol-1 nm6]½ I=IAC[N] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 TYPE[N] O OM OA OE OW N NT NL NR NZ NE C CH0 CH1 CH2 CH3 CH4 CH2r CR1 HC H DUM S CU1+ CU2+ FE ZN2+ MG2+ CA2+ P, SI AR F CL BR CMet OMet NA+ CL- 0.04756 0.04756 0.04756 0.04756 0.05116 0.04936 0.04936 0.04936 0.04936 0.04936 0.04936 0.04838 0.04896 0.07790 0.08642 0.09805 0.1148 0.08564 0.07425 0.009200 0.0 0.0 0.09992 0.02045 0.02045 0.0 0.02045 0.008080 0.03170 0.1214 0.07915 0.03432 0.09362 0.16630 0.09421 0.04756 0.0088792 0.11318 10-3[kJmol-1 nm12]½ 1 1.000 0.8611 1.100 1.100 1.623 1.523 1.523 1.523 1.523 1.523 1.523 2.222 14.33 9.850 5.828 5.162 5.862 5.297 3.888 0.1230 0.0 0.0 3.616 0.07159 0.07159 0.0 0.09716 0.05838 0.7057 4.711 3.138 0.8722 3.911 8.092 4.400 1.525 0.2700 7.776 12 2 1.130 1.841 1.227 1.227 1.623 1.943 2.250 3.068 1.841 2.148 1.984 0.2250 0.4091 0.0 0.09716 0.05838 0.7057 4.711 1.227 1.525 0.2700 7.776 3 3.068 7.776 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 CChl CLChl HChl SDmso CDmso ODmso CCl4 CLCl4 FTfe CTfe CHTfe OTfe CUrea OUrea NUrea CH3p 0.051292 0.091141 0.0061400 0.10277 0.098050 0.047652 0.051292 0.087201 0.034320 0.048380 0.084290 0.047560 0.069906 0.048620 0.057903 0.09805 2.0160 3.7101 0.065574 4.6366 5.1620 0.86686 2.7568 3.5732 1.0000 1.8370 5.0770 1.2270 3.6864 1.2609 1.9877 5.162 13 1.1250 1.0000 1.2270 1.2609 1.9877 - - Table 2.5.6.2.3 GROMOS 53B6 (vacuo) normal van der Waals parameters integer atom code atom type (C12(I,I))½ (C6(I,I))½ [kJmol-1nm6]½ I=IAC[N] 2 8 TYPE[N] OM NL 0.04756 (23.25) 0.04936 (24.13) 10-3[kJmol-1nm12]½ 1 0.8611 (421.0) 1.301 (636.0) 14 2 1.125 (550.0) 1.943 (950.0) 3 1.125 (550.0) - Table 2.5.6.2.4 Selection of van der Waals (repulsive) (C12(I,I))½ parameters J I 1 O 2 OM 3 OA 4 OE 5 OW 6 N 7 NT 8 NL 9 NR 10 NZ 11 NE 24 CU1+ 25 CU2+ 26 FE 27 ZN2+ 28 MG2+ 29 CA2+ 30 P,SI 32 F 33 34 CL 36 OMet 37 NA+ BR 38 CL- 44 47 ODmso 50 52 53 54 OTfe FTfe OUrea NUrea CH3p 1 2 3 4 5 6 7 8 9 10 11 24 25 26 27 28 29 30 32 33 34 36 37 38 44 47 50 52 53 54 O OM OA OE OW N NT NL NR NZ NE CU1+ CU2+ FE ZN2+ MG2+ CA2+ P,SI F CL BR OMet NA+ CL- ODmso FTfe OTfe OUrea NUrea CH3p 1 1 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 2 2 1 1 1 1 1 2 1 1 1 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 2 2 1 1 1 1 1 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 1 1 2 2 2 2 2 2 2 2 1 1 1 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 2 2 1 1 1 1 1 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 1 1 2 2 2 2 2 2 2 2 1 1 2 2 2 2 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1 2 1 2 2 2 1 2 2 1 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 2 1 1 2 1 2 2 2 2 2 2 1 2 3 2 2 2 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1 2 1 3 2 2 1 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 1 1 2 2 2 2 2 2 2 2 1 2 3 2 2 2 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1 2 1 3 2 2 1 2 2 1 2 3 2 2 2 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1 2 1 3 2 2 1 2 2 1 2 3 2 2 2 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 2 1 3 2 2 1 2 1 1 2 3 2 2 2 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 2 1 3 2 2 1 2 1 1 2 3 2 2 2 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 2 1 3 2 2 1 2 1 1 2 3 2 2 2 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 2 1 3 2 2 1 2 1 1 2 3 2 2 2 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 2 1 3 2 2 1 2 1 1 2 3 2 2 2 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 2 1 3 2 2 1 2 1 1 2 3 2 2 2 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 2 1 3 2 2 1 2 1 1 1 1 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 2 2 1 1 1 1 1 2 1 1 1 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 2 2 1 1 1 1 1 2 1 1 1 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 2 2 1 1 1 1 1 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 1 1 2 2 2 2 2 2 2 2 1 2 3 2 2 2 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 2 1 3 2 2 1 2 1 1 1 1 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 2 2 1 1 1 1 1 2 1 1 1 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 2 2 1 1 1 2 1 2 1 1 1 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 2 2 1 1 1 1 1 2 1 1 1 2 1 2 1 2 1 2 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 2 1 2 2 2 1 1 1 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 2 2 1 1 1 2 1 2 1 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 2 1 1 2 1 2 2 2 2 2 2 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Table 2.5.6.2.5 GROMOS 54A7 normal van der Waals parameters for mixed atom type pairs (I,J) integer atom code I atom type 39 39 40 CChl CChl CLChl integer atom code J atom type C6(I,J) C12(I,J) 10-6kJmol-1nm12 40 41 41 CLChl HChl HChl 10-3kJmol1nm6 4.6754 0.3622 0.6493 16 7.4813 0.1745 0.3266 Table 2.5.6.3.1 GROMOS 54A7/54B7 third-neighbour van der Waals parameters integer atom code atom type (C12(I,I))½ (C6(I,I))½ [kJmol-1nm6]½ I=IAC[N] 1 3 4 6 7 8 9 10 11 12 13 14 15 16 18 19 54 TYPE[N] O OA OE N NT NL NR NZ NE C CH0 CH1 CH2 CH3 CH2r CR1 CH3p 10-3[kJmol-1nm12]½ 1 0.8611 1.125 1.125 1.301 1.301 1.301 1.301 1.301 1.301 1.837 1.837 1.933 2.178 2.456 2.178 2.886 2.456 0.04756 0.04756 0.04756 0.04936 0.04936 0.04936 0.04936 0.04936 0.04936 0.04838 0.04838 0.05396 0.06873 0.08278 0.06873 0.07435 0.08278 17 2 - 3 - Table 2.5.6.5.1 GROMOS 54A7 (54B7) atomic charges and charge group definitions for amino acid residues atom name N H C O CD NE HE CZ NH1/2 HH11/12/21/22 NE HE CZ NH1 HH1 NH2 HH21/22 CG, CD OD1, OE1 ND2, NE2, NZ HD21/22, HE21/22, HZ1/2 CG, CD OD1/2, OE1/2 CG, CD OD1, OE1 OD2, OE2 HD2, HE2 CB SG CB SG HG CG ND1 HD1 CD2 HD2 CE1 HE1 NE2 CG ND1 CD2 charge in e -0.310 0.310 0.450 -0.450 0.090 (0.0) -0.110 (-0.240) 0.240 (0.240) 0.340 (0.0) -0.260 (-0.480) 0.240 (0.240) -0.310 0.310 0.266 -0.674 0.408 -0.880 0.440 0.290 -0.450 -0.720 0.440 0.270 (0.720) -0.635 (-0.360) 0.330 -0.450 -0.288 0.408 -0.100 (0.200) -0.400 (-0.200) 0.150 -0.370 0.220 0.0 -0.050 0.310 0.0 0.140 0.0 0.140 -0.540 0.0 -0.540 0.0 18 occurring in all residues all residues Arg (charge +1) Argn (neutral) Argn (neutral) Argn (neutral) Asn, Gln Asn, Gln Asp, Glu (charge -1) Asph, Gluh Cys (charge -.5) Cysh Hisa (proton at D1) Hisb (proton at E2) HD2 CE1 HE1 NE2 HE2 CG ND1 HD1 CD2 HD2 CE1 HE1 NE2 HE2 CG, CB, CB OD1, OG, OG1 HD1, HG, HG1 CE NZ HZ1/2/3 CE NZ HZ1/2 CG /CE SD CG CD1 HD1 CD2 NE1 HE1 CE2 CZ OH HH C 0.140 0.0 0.140 -0.050 0.310 -0.050 (0.0) 0.380 (-0.300) 0.300 (0.300) -0.100 (.0) 0.100 -0.340 (0.0) 0.100 0.310 (-0.300) 0.300 (0.300) 0.266 -0.674 0.408 0.127 (0.0) 0.129 (-0.744) 0.248 (0.248) -0.220 -0.660 0.440 0.241 -0.482 -0.210 -0.140 0.140 0.0 -0.100 0.310 0.0 0.203 -0.611 0.408 -0.140 H C 0.140 0.0 CH2 0.0 Hish (charge +1) Hyp, Ser, Thr Lysh (charge +1) Lys (neutral) Met Trp Tyr all aromatic C-H groups in Phe, Tyr, Trp aromatic C connected to an aliphatic CHn in Phe, Tyr aliphatic CHn connected to aromatic C in Phe, Tyr The charges for the 53B6 force field are given between parentheses. The atoms that are not listed have zero partial charge and form single atom or multiple atom charge groups. 19 Table 2.5.6.2 GROMOS 54A7 atomic charges for various (co)solvents atom name OW HW1/2 charge in e -0.82000 0.41000 occurring in H2O (SPC model) OW HW1/2 -0.84760 0.42380 H2O (SPC/E model) OW HW1/2 -0.68850 0.34425 H2O (SPC/L model) CChl CLChl HChl 0.17900 -0.08700 0.08200 Chloroform SDmso CDmso ODmso 0.12753 0.16000 -0.44753 DMSO CMet OMet HMet 0.26600 -0.67400 0.40800 Methanol CCl4 CLCl4 0.0 0.0 Carbontetrachloride FTFE CTFE CHTFE OTFE HTFE -0.17000 0.45200 0.27300 -0.62500 0.41000 2,2,2-Trifluoroethanol CUrea OUrea NUrea HUrea 0.14200 -0.39000 -0.54200 0.33300 Urea 20 Table 2.5.6.5.3 GROMOS 54A7 (54B7) atomic charges and charge group definitions for nucleotides atom name O3/5* P O1/2P C4* O4* C1* N9, N9, N1, N1, N1 C4, C4 C6, C6, C6 H6, H6, H6 N1, N3, N7, N3, N7, N3 C2, C8, C8 H2, H8, H8 C6, C2, C4 N6, N2, N4 H61/62, H21/22, H41/42 N1, N3, N3 H1, H3, H3 C6, C2, C2, C4, C2, C4 O6, O2, O2, O4, O2, O4 C5, C5 H5, H5 charge in e -0.360 (-0.360) 0.990 (1.440) -0.635 (-0.360) 0.160 -0.360 0.200 -0.200 0.200 0.100 0.100 -0.540 0.440 0.100 0.540 -0.830 0.415 -0.310 0.310 0.450 -0.450 -0.100 0.100 21 occurring in all nucleotides all nucleotides dAde, dGua, dCyt, dThy, Ura dAde, dGua dCyt, dThy, Ura dCyt, dThy, Ura dAde, dAde, dAde, dGua, dGua, dGua, dCyt dAde, dAde, dGua dAde, dAde, dGua dAde, dGua, dCyt dAde, dGua, dCyt dAde, dGua, dCyt dGua, dThy, Ura dGua, dThy, Ura dGua, dCyt, dThy, dThy, Ura, Ura dGua, dCyt, dThy, dThy, Ura, Ura dCyt, Ura dCyt, Ura Table 2.5.6.5.4 GROMOS 54A7 (54B7) atomic charges and charge group definitions for lipids atom name C32, C33, C34, C35 N C31 O31, O32 O33, O34 P C3 C1, C2 O11, O21 O12, O22 C11, C21 C12, …, C22, … charge in e 0.250 0.0 0.0 -0.360 -0.635 0.990 0.0 0.160 -0.360 -0.380 0.580 0.0 occurring in dppc dppc dppc dppc dppc dppc dppc dppc dppc dppc dppc dppc 22 Table 2.5.6.5.5 GROMOS 54A7 (54B7) atomic charges and charge group definitions for carbohydrates atom name C1, C2, C3, C6 O2, O3, O6 HO2, HO3, HO6 C5 O5 O1 C4 C6 O61, O62 C1 O1 CM (methyl) charge in e 0.232 occurring in glucopyranose, polyuronate, terminal – CHn – On – Hn group glucopyranose, polyuronate, terminal – CHn – On – Hn group glucopyranose, polyuronate, terminal – CHn – On – Hn group glucopyranose, polyuronate glucopyranose, polyuronate glucopyranose, polyuronate glucopyranose, polyoronate polyuronate polyuronate terminal – C1 – O1 – CM group terminal – C1 – O1 – CM group terminal – C1 – O1 – CM group -0.642 0.410 0.376 -0.480 -0.360 0.232 0.360 -0.680 0.232 -0.360 0.232 23 Table 4.2.1 54A7 Solute building blocks Name Description (charges in e) amino acids and analogues (L if not indicated otherwise) ALA Alanine ARG Arginine (protonated; charge +1) ARGN Arginine (deprotonated; neutral) ASN Asparagine ASN1 Asparagine (coordinated with ZN) ASP Aspartic acid (deprotonated; charge -1) ASPH Aspartic acid (protonated; neutral) CYS Cysteine (deprotonated; charge -1/2) CYSH Cysteine (protonated; neutral) CYS1 Cysteine (1st member of S-S bridge) CYS2 Cysteine (2nd member of S-S bridge) GLN Glutamine GLU Glutamic acid (deprotonated; charge -1) GLUH Glutamic acid (protonated; neutral) GLY Glycine HISA Histidine (protonated at ND1; neutral) HISB Histidine (protonated at NE2; neutral) HISH Histidine (protonated at ND1 and NE2; charge +1) HIS1 Histidine (coupled to HEME at NE2; neutral) HIS2 Histidine (coupled to HEMC at NE2; neutral) HYP Hydroxyproline ILE Isoleucine LEU Leucine LYS Lysine (deprotonated; neutral) LYSH Lysine (protonated; charge +1) MET Methionine PHE Phenylalanine PRO Proline SER Serine THR Threonine TRP Tryptophan TYR Tyrosine VAL Valine DALA D-Alanine ABU L-2-amino-butanoic acid AIB -methylalanine MEBMT (4R)-4-[(E)-2-butanyl]-4, N-dimethyl-L-threonine 24 MELEU MEVAL SAR N-methyl-L-leucine N-methyl-L-valine Sarcosine or N-methylglycine nucleotides DADE DGUA DCYT DTHY ADE GUA CYT URA 2'-deoxyadenosine 5'-phosphoric acid | 2'-deoxyguanosine 5'-phosphoric acid | (DNA; charge -1) 2'-deoxycytidine 5'-phosphoric acid | 2'-deoxythymidine 5'-phosphoric acid | adenosine 5'-phosphoric acid | guanosine 5'-phosphoric acid |(RNA; charge -1) cytidine 5'-phosphoric acid | uridine 5'-phosphoric acid | FMNO PFN flavin mononucleotide (oxydized, deprotonated at FN5 and FN1; charge -1, OPOHO2-) flavin mononucleotide (semi-reduced, protonated at FN5; charge -1, OPOHO2- ) flavin mononucleotide (reduced, protonated at FN5 and FN1; charge -1, OPOHO2- ) proflavin (protonated at FN5; charge +1) NADP NADH NDPH NDPP NDPHN nicotinamide adenine dinucleotide (NAD+; charge -1) nicotinamide adenine dinucleotide (NADH; charge -2) nicotinamide adenine dinucleotide phosphate (NADPH; charge -3, OPOHO2-) nicotinamide adenine dinucleotide phosphate (NADP+; charge -2, OPOHO2-) nicotinamide adenine dinucleotide phosphate (NADPH; neutral, OPO(OH)2 ) sugars GLCA GLCB GALA GALB MANA MANB TRH UGLB UMNB UGAA UGUA -D-glucopyranosyl (1-4 linkage; neutral) -D-glucopyranosyl (1-4 linkage; neutral) -D-galactopyranosyl (1-4 linkage; neutral) -D-galactopyranosyl (1-4 linkage; neutral) -D-mannoopyranosyl (1-4 linkage; neutral) -D-mannoopyranosyl (1-4 linkage; neutral) trehalose -D-glucuronan (1-4 linkage; neutral) -D-mannuronan (1-4 linkage; neutral) -D-galacturonan (1-4 linkage; neutral) -L-guluronan (1-4 linkage; neutral) lipids DPPC Dipalmitoylphosphatidylcholine (neutral) FMNS FMNR 25 other molecules HEME heme group (charge -2, acidic groups deprotonated) HEMC heme group with bound CO (charge –2, acidic groups deprotonated) CYT* 3',5'-O-(tetra isopropyl-1,3-disiloxanediyl) cytidine (neutral) MTXH FOL DHF THF TMP TMPH TMPHP methotrexate (protonated at N1; charge -2) folate (charge -2) 7,8-dihydrofolate (charge -2) 5,6,7,8-tetrahydrofolate (charge -2) trimethoprim (deprotonated at N1; neutral) trimethoprim (protonated at N1; neutral) trimethoprim (protonated at N1; charge +1) PDG ATP 3-phospho-D-glycerate (charge -2) adenosine 5'-triphosphate (ATP; charge -3) PMB PMBH BA p-methylbenzyl alcoholate (charge -1) p-methylbenzyl alcohol (neutral) benzoic acid RTOL retinol (neutral) TEMP ETH ETHH tetramethyl pyrrolinyl (nitroxide spin label; neutral) ethyl alcoholate (charge -1) ethyl alcohol (neutral) CH4 AR methane (united atom) argon ions SO42ZN2+ NA+ CLCA2+ MG2+ CU1+ CU2+ SO42- ion zinc ion sodium ion chlorine ion calcium ion magnesium ion copper ion copper ion (co)solvents H2O H2OE CHCL3 DMSO water (SPC model, rigid, [81.4] ) water (SPC/E model, rigid, [87.5] ) chloroform (rigid, [94.36] ) dimethylsulfoxide (rigid, [04.6] ) (charge -2) (charge +2) (charge +1) (charge -1) (charge +2) (charge +2) (charge +1) (charge +2) 26 CH3OH CCL4 TFE UREA methanol (rigid ) [00.9] carbontetrachloride (rigid, [96.33] ) 2,2,2-trifluoroethanol (flexible, [00.34]) Urea (flexible, [04.5]) 27 Table 4.2.2 54A7 Solvent building blocks Name H2O H2OE H2OL CHCL3 DMSO CH3OH CCL4 *) Description water (SPC model, [81.4]) water (SPC/E model, [87.5]) water (SPC/L model [02.18])* chloroform ( [94.36] ) dimethylsulfoxide ( [04.6] ) methanol [00.9] carbontetrachloride ( [96.33] ) There is no building block for SPC/L in the 53A5 force field, because it requires an additional atom type. We suggest to use atom type 22 (DUM) for the hydrogens with van der Waals parameters C6(22,22) ½ = 0.53 [kJ mol-1 nm6]½ and C12(22,22)½ = 0. The constraints should be set to rOH = 0.11 nm and rHH = 0.173952 nm. 28 Table 4.2.3 54A7 End group building blocks Name Description proteins and peptides NH3+ N-terminus NH2 N-terminus NPRO N-terminus for proline COOO-terminus COOH O-terminus (charge +1) (neutral) (charge +1) (charge -1) (neutral) nucleic acids D5OH 5’-terminal of DNA D3OH 3’-terminal of DNA 3OH 3’-terminal of RNA (neutral) (neutral) (neutral) sugars C1OH C1OC COHT -C1-O1-H1 group for carbohydrates (neutral) -C1-O1-CH3 group for carbohydrates (neutral) -Cn-On-Hon gropu for carbohydrates(neutral) 29