* Topology file for proteins in coarse-grain representation. * * Each amino acid is represented by two beads, * except the GLY, which is represented by one bead. * * For all amino-acids except GLY * one bead corresponds to the backbone atoms, * and another to the side-chain atoms. * * Also has topology for some lipids and ions * * Made by TCBG, UIUC. 27 1 MASS 1 Nx 72.00000 MASS 2 C 72.00000 MASS 3 P 72.00000 MASS 4 Qa 72.00000 MASS 5 Qd 72.00000 MASS 6 Na 72.00000 MASS 7 Nxx 56.04400 ! Bead for the protein backbone. MASS 8 Ca 15.03500 ! Bead for the side-chain of Alanine. MASS 9 Qdr 100.14500 ! Bead for the side-chain of Arginine. MASS 10 Nxn 58.06000 ! Bead for the side-chain of Asparagine. MASS 11 Qad 58.03600 ! Bead for the side-chain of Aspartate. MASS 12 Pc 47.09500 ! Bead for the side-chain of Cysteine. MASS 13 Nxq 72.08700 ! Bead for the side-chain of Glutamine. MASS 14 Qae 72.06300 ! Bead for the side-chain of Glutamate. MASS 15 Ph 81.09800 ! Bead for the side-chain of Histidine, both -d and -e. MASS 16 Qdh 82.10600 ! Bead for the side-chain of Histidine, protonated. MASS 17 Ci 57.11600 ! Bead for the side-chain of Isoleucine. MASS 18 Cl 57.11600 ! Bead for the side-chain of Leucine. MASS 19 Qdk 73.13900 ! Bead for the side-chain of Lysine. MASS 20 Cm 75.14900 ! Bead for the side-chain of Methionine. MASS 21 Cf 91.13300 ! Bead for the side-chain of Phenilalanine. MASS 22 Cp 42.08100 ! Bead for the side-chain of Proline. MASS 23 Ps 31.03400 ! Bead for the side-chain of Serine. MASS 24 Pt 45.06100 ! Bead for the side-chain of Threonine. MASS 25 Cw 130.17000 ! Bead for the side-chain of Tryptophan. MASS 26 Nxy 107.13200 ! Bead for the side-chain of Tyrosine. MASS 27 Cv 43.08900 ! Bead for the side-chain of Valine. MASS 28 Nap 55.03600 ! Bead for the back-bone of Proline. MASS 29 No 72.00000 ! Nonpolar bead MASS 30 Nd 72.00000 ! Nonpolar HB donor bead MASS 32 Qo 72.00000 ! Charged bead MASS 31 Qx 72.00000 ! Charged HB donor/acceptor bead MASS 32 Nxg 56.04400 ! Bead for the glycine backbone. MASS 33 Cdb 72.00000 ! Apolar bead, double bond. DEFA FIRS NONE LAST NONE AUTO ANGLES DIHE RESI PCGL 0.00 GROUP ATOM CHO Qo 0.70 ! Choline head group ATOM PHO Qa -0.70 ! Phosphate ATOM ES1 Na 0.00 ! Ester group ATOM ES2 Na 0.00 ! Ester group ATOM M1 C 0.00 ! lipid tail ATOM M2 C 0.00 ! lipid tail ATOM M3 C 0.00 ! lipid tail ATOM MT1 C 0.00 ! lipid tail terminus ATOM M4 C 0.00 ! lipid tail ATOM M5 C 0.00 ! lipid tail ATOM M6 C 0.00 ! lipid tail ATOM MT2 C 0.00 ! lipid tail terminus BOND CHO PHO PHO ES1 ES1 ES2 ES1 M1 BOND M1 M2 M2 M3 M3 MT1 ES2 M4 BOND M4 M5 M5 M6 M6 MT2 RESI POPC 0.00 GROUP ATOM CHO Qo 0.70 ! Choline head group ATOM PHO Qa -0.70 ! Phosphate ATOM ES1 Na 0.00 ! Ester group ATOM ES2 Na 0.00 ! Ester group ATOM ME1 C 0.00 ! lipid tail ATOM ME2 C 0.00 ! lipid tail ATOM ME3 C 0.00 ! lipid tail ATOM MT1 C 0.00 ! lipid tail terminus ATOM ME4 C 0.00 ! lipid tail ATOM ME5 C 0.00 ! lipid tail ATOM ME6 C 0.00 ! lipid tail ATOM MT2 C 0.00 ! lipid tail terminus BOND CHO PHO PHO ES1 ES1 ES2 ES1 ME1 BOND ME1 ME2 ME2 ME3 ME3 MT1 ES2 ME4 BOND ME4 ME5 ME5 ME6 ME6 MT2 RESI DOPE 0.00 GROUP ATOM NH3 Qx 0.70 ! Choline head group ATOM PO4 Qa -0.70 ! Phosphate ATOM GL1 Na 0.00 ! Ester group ATOM GL2 Na 0.00 ! Ester group ATOM C1A C 0.00 ! lipid tail ATOM C2A C 0.00 ! lipid tail ATOM D3A C 0.00 ! lipid tail ATOM C4A C 0.00 ! lipid tail terminus ATOM C5A C 0.00 ! lipid tail ATOM C1B C 0.00 ! lipid tail ATOM C2B C 0.00 ! lipid tail ATOM D3B C 0.00 ! lipid tail terminus ATOM C4B C 0.00 ! lipid tail terminus ATOM C5B C 0.00 ! lipid tail terminus BOND NH3 PO4 PO4 GL1 GL1 GL2 GL1 C1A BOND C1A C2A C2A D3A D3A C4A C4A C5A BOND GL2 C1B C1B C2B C2B D3B D3B C4B BOND C4B C5B RESI POPE 0.00 GROUP ATOM ETA Qd 0.70 ! ETA head group ATOM PHO Qa -0.70 ! Phosphate ATOM ES1 Na 0.00 ! Ester group ATOM ES2 Na 0.00 ! Ester group ATOM ME1 C 0.00 ! lipid tail ATOM ME2 Cdb 0.00 ! lipid tail, double bond ATOM ME3 C 0.00 ! lipid tail ATOM MT1 C 0.00 ! lipid tail terminus ATOM ME4 C 0.00 ! lipid tail ATOM ME5 C 0.00 ! lipid tail ATOM ME6 C 0.00 ! lipid tail ATOM MT2 C 0.00 ! lipid tail terminus BOND ETA PHO PHO ES1 ES1 ES2 ES1 ME1 BOND ME1 ME2 ME2 ME3 ME3 MT1 ES2 ME4 BOND ME4 ME5 ME5 ME6 ME6 MT2 RESI DOPC 0.00 GROUP ATOM CHO Qo 0.70 ! Choline head group ATOM PHO Qa -0.70 ! Phosphate ATOM ES1 Na 0.00 ! Ester group ATOM ES2 Na 0.00 ! Ester group ATOM ME1 C 0.00 ! lipid tail ATOM ME2 C 0.00 ! lipid tail ATOM MD3 Cdb 0.00 ! lipid tail ATOM MT1 C 0.00 ! lipid tail terminus ATOM ME4 C 0.00 ! lipid tail ATOM ME5 C 0.00 ! lipid tail ATOM MD6 Cdb 0.00 ! lipid tail terminus ATOM MT2 C 0.00 ! lipid tail terminus BOND CHO PHO PHO ES1 ES1 ES2 ES1 ME1 BOND ME1 ME2 ME2 MD3 MD3 MT1 ES2 ME4 BOND ME4 ME5 ME5 MD6 MD6 MT2 RESI DOPS -0.70 GROUP ATOM SHO P 0.00 ! Serine head group ATOM PHO Qa -0.70 ! Phosphate ATOM ES1 Na 0.00 ! Ester group ATOM ES2 Na 0.00 ! Ester group ATOM ME1 C 0.00 ! lipid tail ATOM ME2 C 0.00 ! lipid tail ATOM MD3 Cdb 0.00 ! lipid tail ATOM MT1 C 0.00 ! lipid tail terminus ATOM ME4 C 0.00 ! lipid tail ATOM ME5 C 0.00 ! lipid tail ATOM MD6 Cdb 0.00 ! lipid tail terminus ATOM MT2 C 0.00 ! lipid tail terminus BOND SHO PHO PHO ES1 ES1 ES2 ES1 ME1 BOND ME1 ME2 ME2 MD3 MD3 MT1 ES2 ME4 BOND ME4 ME5 ME5 MD6 MD6 MT2 RESI DPC 0.00 GROUP ATOM NC3 Qo 0.70 ! Choline ATOM PO4 Qa -0.70 ! Phosphate ATOM C1 C 0.00 ATOM C2 C 0.00 ATOM C3 C 0.00 BOND NC3 PO4 PO4 C1 C1 C2 C2 C3 RESI SOD 0.7 GROUP ATOM SOD Qd 0.7 RESI CHL -0.7 GROUP ATOM CHL Qa -0.7 RESI ALA 0.00 ATOM BB Nxx 0.00 ATOM ALA2 Ca 0.00 BOND BB ALA2 BB +BB RESI ARG 0.70 ATOM BB Nxx 0.00 ATOM ARG2 Qdr 0.70 BOND BB ARG2 BB +BB RESI ASN 0.00 ATOM BB Nxx 0.00 ATOM ASN2 Nxn 0.00 BOND BB ASN2 BB +BB RESI ASP -0.70 ATOM BB Nxx 0.00 ATOM ASP2 Qad -0.70 BOND BB ASP2 BB +BB RESI CYS 0.00 ATOM BB Nxx 0.00 ATOM CYS2 Pc 0.00 BOND BB CYS2 BB +BB RESI GLN 0.00 ATOM BB Nxx 0.00 ATOM GLN2 Nxq 0.00 BOND BB GLN2 BB +BB RESI GLU -0.70 ATOM BB Nxx 0.00 ATOM GLU2 Qae -0.70 BOND BB GLU2 BB +BB RESI GLY 0.00 ATOM BB Nxg 0.00 BOND BB +BB RESI HSD 0.00 ! neutral HIS, proton on ND1 ATOM BB Nxx 0.00 ATOM HSD2 Ph 0.00 BOND BB HSD2 BB +BB RESI HSE 0.00 ! neutral His, proton on NE2 ATOM BB Nxx 0.00 ATOM HSE2 Ph 0.00 BOND BB HSE2 BB +BB RESI HSP 0.70 ! Protonated His ATOM BB Nxx 0.00 ATOM HSP2 Qdh 0.70 BOND BB HSP2 BB +BB RESI ILE 0.00 ATOM BB Nxx 0.00 ATOM ILE2 Ci 0.00 BOND BB ILE2 BB +BB RESI LEU 0.00 ATOM BB Nxx 0.00 ATOM LEU2 Cl 0.00 BOND BB LEU2 BB +BB RESI LYS 0.70 ATOM BB Nxx 0.00 ATOM LYS2 Qdk 0.70 BOND BB LYS2 BB +BB RESI MET 0.00 ATOM BB Nxx 0.00 ATOM MET2 Cm 0.00 BOND BB MET2 BB +BB RESI PHE 0.00 ATOM BB Nxx 0.00 ATOM PHE2 Cf 0.00 BOND BB PHE2 BB +BB RESI PRO 0.00 ATOM BB Nap 0.00 ATOM PRO2 Cp 0.00 BOND BB PRO2 BB +BB RESI SER 0.00 ATOM BB Nxx 0.00 ATOM SER2 Ps 0.00 BOND BB SER2 BB +BB RESI THR 0.00 ATOM BB Nxx 0.00 ATOM THR2 Pt 0.00 BOND BB THR2 BB +BB RESI TRP 0.00 ATOM BB Nxx 0.00 ATOM TRP2 Cw 0.00 BOND BB TRP2 BB +BB RESI TYR 0.00 ATOM BB Nxx 0.00 ATOM TYR2 Nxy 0.00 BOND BB TYR2 BB +BB RESI VAL 0.00 ATOM BB Nxx 0.00 ATOM VAL2 Cv 0.00 BOND BB VAL2 BB +BB RESI TIP3 0.00 ! ATOM H2O P 0.00 ! DONOR H2O ACCEPTOR H2O END