; ; parameterization Benoit Roux and MacKerell ; J. Phys. Chem. B, 2007, 111 (11), pp 2873-2885 ; http://pubs.acs.org/doi/full/10.1021/jp0663614 ; ; Unit transition ; 1 Kj/mol = 4.18400 Kcal/mol ; Precision "3.3996700e-01" ; ;q(C_P)=q(C)-q(D) ; q(D)^2 =2*Kd[charmm]*alpha[charmm]/(138.935485/4.184*10); ;the factor "2" appears in the relation for the q(d)^2 because energy of the spring is represented in charmm as Kd*x^2 [ atomtypes ] ; ; SOLVENT TYPES ;name mass charge ptype sigma eps [kj/mol] CA_P 11.611 1.9556282e+00 A 3.5635948e-01 2.84512e-01 ; m(C)=12.011 m(D)=0.4 ; m(CA_P)=m(C)-m(DR_C) DR_C 0.400 -2.0356282e+00 A 0.0000000e+00 0.00000e+00 ; Rmin(CA)/2=0.2nm, Rmin(HA)/2=0.13nm ; sigma=(Rmin/2)*2/2^(1/6)=(Rmin/2)*1.7818 HA_P 1.008 0.080 A 2.3163366e-01 1.79912e-01 ; eps(CA)=0.068, eps(HA)=0.043 Kj/mol ; eps[gmx]=-eps[charmm]*4.18400 [ moleculetype ] ; molname nrexcl BNZ 2 [ atoms ] ; id at type resnr resnm atnm cg nr charge mass 1 CA_P 1 BNZ C1 1 ; 1.3594 12.011 ; qtot 1.359 2 DR_C 1 BNZ D1 1 ; -1.4394 1.008 ; qtot -0.08 3 HA_P 1 BNZ H1 1 ; 0.08 1.008 ; qtot 0 4 CA_P 1 BNZ C2 2 ; 1.3594 12.011 ; qtot 1.359 5 DR_C 1 BNZ D2 2 ; -1.4394 1.008 ; qtot -0.08 6 HA_P 1 BNZ H2 2 ; 0.08 1.008 ; qtot 0 7 CA_P 1 BNZ C3 3 ; 1.3594 12.011 ; qtot 1.359 8 DR_C 1 BNZ D3 3 ; -1.4394 1.008 ; qtot -0.08 9 HA_P 1 BNZ H3 3 ; 0.08 1.008 ; qtot 0 10 CA_P 1 BNZ C4 4 ; 1.3594 12.011 ; qtot 1.359 11 DR_C 1 BNZ D4 4 ; -1.4394 1.008 ; qtot -0.08 12 HA_P 1 BNZ H4 4 ; 0.08 1.008 ; qtot 0 13 CA_P 1 BNZ C5 5 ; 1.3594 12.011 ; qtot 1.359 14 DR_C 1 BNZ D5 5 ; -1.4394 1.008 ; qtot -0.08 15 HA_P 1 BNZ H5 5 ; 0.08 1.008 ; qtot 0 16 CA_P 1 BNZ C6 6 ; 1.3594 12.011 ; qtot 1.359 17 DR_C 1 BNZ D6 6 ; -1.4394 1.008 ; qtot -0.08 18 HA_P 1 BNZ H6 6 ; 0.08 1.008 ; qtot 0 [ polarization ] ;ai aj type alpha(nm^3) 1 2 1 1.376e-03 4 5 1 1.376e-03 7 8 1 1.376e-03 10 11 1 1.376e-03 13 14 1 1.376e-03 16 17 1 1.376e-03 ; dipole-dipole interaction in Gromacs: ; Vthole=q(i)*q(j)/r(ij)*[1-(1+s(ij)/2)*exp(-s(ij))]; where s(ij)=a*r(ij)/(alpha(i)alpha(j))^(1/6) ; CHARMM documentation http://www.charmm.org/html/documentation/c32b2/drude.html ; only charges {q(drude),-q(drude)} interacts between each other but not {q(drude),-q(havy)} [ thole_polarization ] ;ai aj func a alpha(i) alpha(j) 1 2 4 5 2 2.6 1.376e-03 1.376e-03 1 2 7 8 2 2.6 1.376e-03 1.376e-03 1 2 16 17 2 2.6 1.376e-03 1.376e-03 1 2 13 14 2 2.6 1.376e-03 1.376e-03 4 5 7 8 2 2.6 1.376e-03 1.376e-03 4 5 10 11 2 2.6 1.376e-03 1.376e-03 4 5 16 17 2 2.6 1.376e-03 1.376e-03 7 8 10 11 2 2.6 1.376e-03 1.376e-03 7 8 13 14 2 2.6 1.376e-03 1.376e-03 10 11 13 14 2 2.6 1.376e-03 1.376e-03 10 11 16 17 2 2.6 1.376e-03 1.376e-03 13 14 16 17 2 2.6 1.376e-03 1.376e-03 ; BONDS ; kb[gmx]=2*kb[paper]*4.184*100, because gmx functional is 1/2*kb(r-b0)^2, also transfer units. ; ; func b0 kb #define b_CC 1 0.1375 255224.0 ;kb[paper]=305.0 Kcal/mol/A^2 #define b_CH 1 0.1080 284512.0 ;kb[paper]=340.0 Kcal/mol/A^2 #define b_DRUDE 5 ; Connect by chemical bond drude to the atom in order to exclude interactions via 'nrexcl=' ; ; !!! ATTENTION !!! ; ; harmonic interaction between drude and atom is taken into account in the field [polarization] ; thus, this interaction should not be doubled in the section [bonds] ;#define b_DRUDE 1 0.0000 418400.0 ;kb[paper]=500.0 Kcal/mol/A^2 [ bonds ] 1 2 b_DRUDE 1 3 b_CH 1 4 b_CC 1 16 b_CC 4 5 b_DRUDE 4 6 b_CH 4 7 b_CC 7 8 b_DRUDE 7 9 b_CH 7 10 b_CC 10 11 b_DRUDE 10 12 b_CH 10 13 b_CC 13 14 b_DRUDE 13 15 b_CH 13 16 b_CC 16 17 b_DRUDE 16 18 b_CH # ifdef PAIRS [ pairs ] ; ai aj func THERE ARE 1-4 INTERACTION 1 8 1 1 9 1 1 10 1 1 14 1 1 15 1 2 5 1 2 6 1 2 7 1 2 13 1 2 17 1 2 18 1 3 5 1 3 6 1 3 7 1 3 13 1 3 17 1 3 18 1 4 11 1 4 12 1 4 13 1 4 17 1 4 18 1 5 8 1 5 9 1 5 10 1 5 16 1 6 8 1 6 9 1 6 10 1 6 16 1 7 14 1 7 15 1 7 16 1 8 11 1 8 12 1 8 13 1 9 11 1 9 12 1 9 13 1 10 17 1 10 18 1 11 14 1 11 15 1 11 16 1 12 14 1 12 15 1 12 16 1 14 17 1 14 18 1 15 17 1 15 18 1 #endif #ifdef NO_UB ; kth[gmx]=2*kth[paper]*4.184, because gmx functional is 1/2*kth(t-t0)^2, also transfer units. ; ; func th0 kth #define a_CCC 1 120.0 334.72 ;kth[paper]=40.0 Kcal/mol/rad^2 #define a_CCH 1 120.0 251.04 ;kth[paper]=30.0 Kcal/mol/rad^2 [ angles ] ; ai aj ak angle 3 1 4 a_CCH 3 1 16 a_CCH 4 1 16 a_CCC 1 4 6 a_CCH 1 4 7 a_CCC 6 4 7 a_CCH 4 7 9 a_CCH 4 7 10 a_CCC 9 7 10 a_CCH 7 10 12 a_CCH 7 10 13 a_CCC 12 10 13 a_CCH 10 13 15 a_CCH 10 13 16 a_CCC 15 13 16 a_CCH 1 16 13 a_CCC 1 16 18 a_CCH 13 16 18 a_CCH #endif ; Urey-Bradley (incorrect!!! need to be clarified), angle type: fun=5; Includes both angel and distance terms ; kth[gmx]=2*kth[paper]*4.184, because gmx functional is 1/2*kth(t-t0)^2, also transfer units. ; kub[gmx]=2*kub[paper]*4.184*100, because gmx functional is 1/2*kub(S-S0)^2, also transfer units. ; ; func th0 kth b0_13 kub #define ub_CCC 5 120.0 334.72 0.24162 29288.0 ;kub[paper]=35.0 Kcal/mol/A^2 #define ub_CCH 5 120.0 251.04 0.21525 18409.6 ;kub[paper]=22.0 Kcal/mol/A^2 [ angles ] ; ai aj ak angle 3 1 4 ub_CCH 3 1 16 ub_CCH 4 1 16 ub_CCC 1 4 6 ub_CCH 1 4 7 ub_CCC 6 4 7 ub_CCH 4 7 9 ub_CCH 4 7 10 ub_CCC 9 7 10 ub_CCH 7 10 12 ub_CCH 7 10 13 ub_CCC 12 10 13 ub_CCH 10 13 15 ub_CCH 10 13 16 ub_CCC 15 13 16 ub_CCH 1 16 13 ub_CCC 1 16 18 ub_CCH 13 16 18 ub_CCH ; Dihedrals ; kdh[gmx]=kdh[paper]*4.184, because gmx functional is kdh*(1+cos(mult*chi-delta)), also transfer units. ; ; func delta kdh mult #define dh_CCCC 1 180.0 11.7152 2 ;kdh[paper]=2.8 Kcal/mol #define dh_CCCH 1 180.0 17.5728 2 ;kdh[paper]=4.2 Kcal/mol #define dh_HCCH 1 180.0 10.0416 2 ;kdh[paper]=2.4 Kcal/mol [ dihedrals ] ; ai aj ak al func 3 1 4 6 dh_HCCH 3 1 4 7 dh_CCCH 16 1 4 6 dh_CCCH 16 1 4 7 dh_CCCC 3 1 16 13 dh_CCCH 3 1 16 18 dh_HCCH 4 1 16 13 dh_CCCC 4 1 16 18 dh_CCCH 1 4 7 9 dh_CCCH 1 4 7 10 dh_CCCC 6 4 7 9 dh_HCCH 6 4 7 10 dh_CCCH 4 7 10 12 dh_CCCH 4 7 10 13 dh_CCCC 9 7 10 12 dh_HCCH 9 7 10 13 dh_CCCH 7 10 13 15 dh_CCCH 7 10 13 16 dh_CCCC 12 10 13 15 dh_HCCH 12 10 13 16 dh_CCCH 10 13 16 1 dh_CCCC 10 13 16 18 dh_CCCH 15 13 16 1 dh_CCCH 15 13 16 18 dh_HCCH ;exclude dipole-dipole interaction between 1-2,1-3 neighbors; Note, Drude should be considered ;as the same partictle to which it is connected ;this interaction should be accounted by THOLE potential (see the field [thole_polarization]) ;bellow we suppose that "moleculetype" is set up to 2 (exclude atoms separated up to 2 bonds) [ exclusions ] 1 8 14 2 5 6 7 8 13 14 17 18 3 5 17 4 11 17 5 8 9 10 11 16 17 2 3 6 8 2 7 14 2 8 11 12 13 14 1 2 5 6 9 11 5 10 17 5 11 14 15 16 17 4 5 8 9 12 14 8 13 2 8 14 17 18 1 2 7 8 11 12 15 17 11 16 5 11 17 2 3 4 5 10 11 14 15 18 2 14