! Parameter file for Retinal protonated schiff base / lysine bound retinal (LYR) ! Converted from AMBER format parameter file (provided by Shig Hayashi) for retinal ! in Bacteriorhodopsin. ! Use at your own risk! ! Compiled by: ! Jan Saam ! Humboldt-University Berlin ! Medizinische Fakultät (Charité) ! Institute for Biochemisty ! Monbijoustr. 2 ! 10117 Berlin ! Germany ! phone: +49 30 450 528 449 ! email: saam@charite.de !!!! Please acknowledge ALL 5 publications: !!!! ! Equilibrium bondlengths and angles: ! ------------------------------------ ! Tajkhorshid, E., B. Paizs, and S. Suhai. 1997. Conformational effects on the proton ! affinity of the schiff base in bacteriorhodopsin: a density functional study. JPCB 101: ! 8021-8028. ! ! Tajkhorshid, E. and S. Suhai. 1999. Influence of the methyl groups on the structure, charge ! distribution and proton affinity of the retinal schiff base. JPCB 103: 5581-5590. ! Dihedral parameters: ! -------------------- ! Tajkhorshid, E., J. Baudry, K. Schulten, and S. Suhai. 2000. Molecular dynamics study of ! the nature and origin of retinal s twisted structure in bacteriorhodopsin. ! Biophys. J. 78:683-693. ! Lennard Jones parameters and charges (NONBONDED section) (ALSO NOTE ALTERNATIVE DIHEDRAL PARAMETERS IN FOLLOWING PUBLICATIONS) ! -------------------------------------------- ! M. Nina et al. (1995), Biophys. J. 68 : 25-39 ! ! J. Baudry, S. Crouzy, B. Roux and J.C. Smith. Quantum chemical and free energy simulation analysis of retinal ! conformational energetics. ! J. Chem. Info. Comput. Sci., 37(1997) 1018-1024 . BONDS NCH1 CT2 340.00 1.49 NCH1 HCR 430.00 1.00 NCH1 CR15 490.00 1.32 CR15 HPL1 370.00 1.07 CR15 CR14 430.00 1.37 CR14 HPL 370.00 1.07 CR14 CR13 550.00 1.40 CR13 CT3 320.00 1.52 CR13 CR12 430.00 1.40 CR12 HPL 370.00 1.07 CR12 CR11 550.00 1.37 CR11 HPL 370.00 1.07 CR11 CR10 430.00 1.41 CR10 HPL 370.00 1.07 CR10 CR9 550.00 1.37 CR9 CT3 320.00 1.52 CR9 CR8 430.00 1.45 CR8 HPL 370.00 1.07 CR8 CR7 550.00 1.34 CR7 HPL 370.00 1.07 CR7 CR6 430.00 1.47 CR6 CT3 320.00 1.54 CR6 CR5 550.00 1.34 CR5 CT3 320.00 1.52 CR5 CT2 320.00 1.52 ANGLES CT2 CT2 NCH1 80.00 111.20 HCR NCH1 CT2 35.00 118.40 CT2 NCH1 CR15 50.00 123.20 CR15 NCH1 HCR 35.00 120.00 HA CT2 NCH1 50.00 109.50 NCH1 CR15 HPL1 35.00 119.10 NCH1 CR15 CR14 95.00 122.90 CR15 CR14 HPL 35.00 119.70 CR14 CR15 HPL1 35.00 119.70 CR15 CR14 CR13 95.00 122.90 CR14 CR13 CT3 70.00 119.70 CR13 CR14 HPL 35.00 119.70 CR13 CT3 HA 50.00 109.50 CR14 CR13 CR12 95.00 122.90 CR13 CR12 HPL 35.00 119.70 CR12 CR13 CT3 70.00 119.70 CR13 CR12 CR11 95.00 122.90 CR12 CR11 HPL 35.00 119.70 CR11 CR12 HPL 35.00 119.70 CR12 CR11 CR10 95.00 122.90 CR11 CR10 HPL 35.00 119.70 CR10 CR11 HPL 35.00 119.70 CR11 CR10 CR9 95.00 122.90 CR10 CR9 CT3 70.00 119.70 CR9 CT3 HA 50.00 109.50 CR9 CR10 HPL 35.00 119.70 CR10 CR9 CR8 95.00 122.90 CR9 CR8 HPL 35.00 119.70 CR8 CR9 CT3 70.00 119.70 CR9 CR8 CR7 95.00 122.90 CR8 CR7 HPL 35.00 119.70 CR7 CR8 HPL 35.00 119.70 CR8 CR7 CR6 95.00 122.90 CR7 CR6 CT3 70.00 119.70 CR6 CR7 HPL 35.00 119.70 CR7 CR6 CR5 95.00 122.90 CR6 CR5 CT3 70.00 119.70 ! ? CR6 CR5 CT2 70.00 119.70 ! ? CT3 CR5 CT2 70.00 119.70 CR5 CT2 HA 50.00 109.50 ! ? CR5 CT3 HA 50.00 109.50 ! ? CR6 CT3 CT2 63.00 111.10 ! ? CR6 CT3 CT3 63.00 111.10 ! ? CR5 CT2 CT2 63.00 111.10 CR5 CR6 CT3 70.00 119.70 CT3 CT3 CT3 63.00 109.50 ! reg. tetrahedron, force CT2 CT3 CT3 63.00 109.50 ! constant from CR5-CT3-CT3 DIHEDRALS X CT2 NCH1 X 0.0 2 0.0 X NCH1 CR15 X 3.6 2 180.0 ! double X CR15 CR14 X 3.8 2 180.0 X CR14 CR13 X 3.68 2 180.0 ! double X CT3 CR13 X 0.0 2 180.0 X CR13 CR12 X 3.54 2 180.0 X CR12 CR11 X 4.385 2 180.0 ! double X CR11 CR10 X 2.81 2 180.0 X CR10 CR9 X 4.66 2 180.0 ! double X CT3 CR9 X 0.0 2 180.0 X CR9 CR8 X 2.13 2 180.0 X CR8 CR7 X 5.0 2 180.0 ! double X CR7 CR6 X 1.405 2 180.0 X CR6 CR5 X 5.0 2 180.0 ! double X CT2 CR5 X 0.0 2 180.0 ! ? X CT3 CR5 X 0.0 2 180.0 ! ? X CT3 CR6 X 0.0 2 180.0 IMPROPER ! !V(improper) = Kpsi(psi - psi0)**2 ! !Kpsi: kcal/mole/rad**2 !psi0: degrees !note that the second column of numbers (0) is ignored ! !atom types Kpsi psi0 ! ! Retinal Protonated Schiff base ! ****************************** ! ! impr parameters ! ! From Nicolas : ! CPB C CPB CPA 90.00 0 0.00 ! similar to CR8 CT CR8 CR7 .... ! CPM3 CPA CPA HA 29.40 0 0.00 ! similar to CR11 HPL CR10 CR12 for example . ! nouvel essai improper redefinis CR15 CR14 NCH1 HPL1 100.00 0 0.000 CR14 CR13 CR15 HPL 100.00 0 0.000 CR13 CR12 CR14 CT3 100.00 0 0.000 CR12 CR11 CR13 HPL 100.00 0 0.000 CR11 CR10 CR12 HPL 100.00 0 0.000 CR10 CR9 CR11 HPL 100.00 0 0.000 CR9 CR8 CR10 CT3 100.00 0 0.00 CR8 CR7 CR9 HPL 100.00 0 0.00 CR7 CR6 CR8 HPL 100.00 0 0.00 CR6 CR5 CR7 CT3 100.00 0 0.00 CR5 CR6 CT2 CT3 100.00 0 0.00 CR6 CT3 CR5 CR7 100.00 0 0.00 CR7 CR8 CR6 HPL 100.00 0 0.00 CR9 CR10 CR8 CT3 100.00 0 0.00 CR11 CR12 CR10 HPL 100.00 0 0.00 CR13 CR14 CR12 CT3 100.00 0 0.00 ! ! Shiff base ! CR15 NCH1 CR14 HPL1 100.000 0 0.000 NCH1 CT2 CR15 HCR 45.000 0 0.000 ! AMIDES PROTON OOP NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j ! !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 ! !NONBON ! CR15 1.9080 0.0860 ! CR14 1.9080 0.0860 ! CR13 1.9080 0.0860 ! CR12 1.9080 0.0860 ! CR11 1.9080 0.0860 ! CR10 1.9080 0.0860 ! CR9 1.9080 0.0860 ! CR8 1.9080 0.0860 ! CR7 1.9080 0.0860 ! CR6 1.9080 0.0860 ! CR5 1.9080 0.0860 ! NCH1 1.8240 0.1700 ! HCR 0.6000 0.0157 ! OW 1.7825 0.2941 ! Van der Waals parameters from Mafalda Nina et al. (1995), ! Biophys. J. 68 : 25-39 CTR 0.000000 -0.156200 1.800000 ! Retinal Schiff base ! methyl group ( idem CT ) Mafalda CR* 0.000000 -0.110000 2.100000 0.000 -0.110000 1.600000 !last 2 v14 ! RETINAL from ab initio calc's (J. Baudry) Sept. 1996 HAR 0.000000 -0.007800 1.468000 ! Retinal Schiff base ! methyl group E-N-methyl-2-propenylidenimine HCR 0.000000 -0.046 0.224500 ! RETINAL from ab initio calc's (Mafalda) HPL 0.000000 -0.046000 0.87000 ! RETINAL from ab initio calc's (Mafalda) HPL1 0.000000 -0.0078000 0.87000 ! RETINAL from ab initio calc's (Mafalda) NCH1 0.000000 -0.200000 1.950000 ! RETINAL from ab initio calc's (Mafalda)