* CHARMM27 Custom Topology File * Custom molecules !Parent files that have to be read prior to using this file !top_all27_na.rtf !par_all27_na.prm 31 1 MASS 197 CSD 12.01100 C ! CO2 carbon MASS 198 SD 32.06000 S ! sulphur PRES 4SU 0.00 ! Make 4-thiouridine out of U DELETE ATOM O4 ATOM S1 SD -0.80 ATOM C4 CSD 0.85 BOND C4 S1 ANGLE C5 C4 S1 N3 C4 S1 DIHE H5 C5 C4 S1 DIHE C6 C5 C4 S1 DIHE H3 N3 C4 S1 DIHE C2 N3 C4 S1 PRES DHU 0.00 ! Make Dihydro-U out of U from toprna10r_22.inp ! === DELETE ATOM H5 DELETE ATOM H6 ATOM C5 CP2 -0.25 ! Change these two Cs to C2 adds the Hs ATOM C6 CP3 0.10 ATOM H51 HA 0.10 ATOM H52 HA 0.10 ATOM H61 HA 0.12 ATOM H62 HA 0.12 BOND C5 H51 C5 H52 C6 H61 C6 H62 ANGLE C4 C5 H52 C4 C5 H51 H51 C5 H52 ANGLE H52 C5 C6 H51 C5 C6 C5 C6 H61 ANGLE C5 C6 H62 H61 C6 H62 H61 C6 N1 ANGLE H62 C6 N1 DELE IMPH N1 C2 N3 C4 ! The ring is no longer aromatic DELE IMPH C2 N3 C4 C5 DELE IMPH N3 C4 C5 C6 DELE IMPH C4 C5 C6 N1 DELE IMPH C5 C6 N1 C2 DELE IMPH C6 N1 C2 N3 DIHE N1 C2 N3 C4 ! So we use plain dihedrals instead DIHE C2 N3 C4 C5 DIHE N3 C4 C5 C6 DIHE C4 C5 C6 N1 DIHE C5 C6 N1 C2 DIHE C6 N1 C2 N3 DIHE O4 C4 C5 H52 DIHE O4 C4 C5 H51 DIHE C4 C5 C6 H62 DIHE C4 C5 C6 H61 DIHE H52 C5 C6 H61 DIHE H52 C5 C6 H62 DIHE H51 C5 C6 H61 DIHE H51 C5 C6 H62 DIHE C2 N1 C6 H62 DIHE C2 N1 C6 H61 ! Pseudouridine RESI PSU -1.00 ! O4 ATOM P P 1.50 ! || ATOM O1P ON3 -0.78 ! C4 H3 ATOM O2P ON3 -0.78 ! / \ / ATOM O5' ON2 -0.57 ! |-----C5 N3 ATOM C5' CN8B -0.08 ! | || | ATOM H5' HN8 0.09 ! | H6-C6 C2 ATOM H5'' HN8 0.09 ! | \ / \\ GROUP ! | N1 O2 ATOM C4' CN7 0.16 ! \ |H1 ATOM H4' HN7 0.09 ! \-------\ ATOM O4' ON6B -0.50 ! \ ATOM C1' CN7 0.11 ! O1P H5' H4' O4' \ ATOM H1' HN7 0.04 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N1 NN2B -0.39 ! | | \ / \ ATOM H1 HN2 0.25 ! ATOM C6 CN3 0.20 ! O2P H5'' C3'--C2' H1' ATOM H6 HN3 0.14 ! / \ / \ ATOM C2 CN1T 0.55 ! O3' H3' O2' H2'' ATOM O2 ON1 -0.45 ! | | ATOM N3 NN2U -0.46 ! H2' ATOM H3 HN2 0.36 ! ATOM C4 CN1 0.53 ! ATOM O4 ON1 -0.48 ! ATOM C5 CN3 -0.15 ! GROUP ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' C5 C1' C2' N1 C2 N1 C6 BOND C2 N3 N3 H3 N3 C4 C4 C5 BOND C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' N1 H1 BOND C5' H5'' C6 H6 C5' H5' DOUBLE C2 O2 C4 O4 C5 C6 IMPR C2 N1 N3 O2 C4 N3 C5 O4 DONO H3 N3 DONO H1 N1 DONO H2' O2' ACCE O2 C2 ACCE O4 C4 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' MASS 303 NN3U 14.00700 N ! Nucleic acid unprotonated ring nitrogen, ura N3 ! Pseudouridine tautomer 4 ! By analogy with PSU and checked with 6-31G* ! A. Black 5/15/2006 RESI PS4 -1.00 ! O4-H4 ATOM P P 1.50 ! | ATOM O1P ON3 -0.78 ! C4 ATOM O2P ON3 -0.78 ! / \\ ATOM O5' ON2 -0.57 ! |-----C5 N3 ATOM C5' CN8B -0.08 ! | || | ATOM H5' HN8 0.09 ! | H6-C6 C2 ATOM H5'' HN8 0.09 ! | \ / \\ GROUP ! | N1 O2 ATOM C4' CN7 0.16 ! \ |H1 ATOM H4' HN7 0.09 ! \-------\ ATOM O4' ON6B -0.50 ! \ ATOM C1' CN7 0.11 ! O1P H5' H4' O4' \ ATOM H1' HN7 0.04 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N1 NN2B -0.49 ! | | \ / \ ATOM H1 HN2 0.26 ! ATOM C6 CN3 0.29 ! O2P H5'' C3'--C2' H1' ATOM H6 HN3 0.14 ! / \ / \ ATOM C2 CN1T 0.73 ! O3' H3' O2' H2'' ATOM O2 ON1 -0.49 ! | | ATOM N3 NN3U -0.62 ! H2' ATOM H4 HN5 0.46 ! ATOM C4 CN1 0.59 ! ATOM O4 ON5 -0.52 ! ATOM C5 CN3 -0.25 ! GROUP ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' C5 C1' C2' N1 C2 N1 C6 N1 H1 BOND C2 N3 C4 C5 C4 O4 O4 H4 BOND C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' BOND C5' H5'' C6 H6 C5' H5' DOUBLE C2 O2 C5 C6 N3 C4 IMPR C2 N1 N3 O2 C4 N3 C5 O4 DONO H1 N1 DONO H2' O2' ACCE O2 C2 ACCE O4 C4 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' ! Master topology file for 1-methylguanine (1mg) ! analogy based on toppar_all27_na_base_modifications.str ! all changes from 1EG ! 3/17/2005 p. o'donoghue RESI 1MG -1.00 ! H1A1 O6 ATOM P P 1.50 ! | || ATOM O1P ON3 -0.78 ! H1A2-C1A C6 ATOM O2P ON3 -0.78 ! | \ / \ ATOM O5' ON2 -0.57 ! H1A3 N1 C5--N7\\ ATOM C5' CN8B -0.08 ! | || C8-H8 ATOM H5' HN8 0.09 ! C2 C4--N9/ ATOM H5'' HN8 0.09 ! / \\ / \ GROUP ! H21-N2 N3 \ ATOM C4' CN7 0.16 ! | \ ATOM H4' HN7 0.09 ! H22 \ ATOM O4' ON6B -0.50 ! \ ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ ATOM H1' HN7 0.09 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N9 NN2B -0.02 ! | | \ / \ ATOM C4 CN5 0.26 ! O2P H5'' C3'--C2' H1' ATOM N2 NN1 -0.68 ! / \ / \ ATOM H21 HN1 0.32 ! O3' H3' O2' H2'' ATOM H22 HN1 0.35 ! | | ATOM N3 NN3G -0.74 ! H2' ATOM C2 CN2 0.75 ATOM N1 NN2G -0.08 ! Aquired +0.26 from H1 in GUA ATOM C1A CN8 -0.27 ! standard methyl addition ATOM H1A1 HN8 0.09 ! ATOM H1A2 HN8 0.09 ! ATOM H1A3 HN8 0.09 ! ATOM C6 CN1 0.54 ATOM O6 ON1 -0.51 ATOM C5 CN5G 0.00 ATOM N7 NN4 -0.60 ATOM C8 CN4 0.25 ATOM H8 HN3 0.16 GROUP ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 C6 C6 C5 BOND C5 N7 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 BOND N1 C1A C1A H1A1 C1A H1A2 C1A H1A3 DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22 DONO H21 N2 DONO H22 N2 DONO H1 N1 DONO H2' O2' ACCE O6 C6 ACCE N3 ACCE N7 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' ! topology entry for 2-methylcytosine (5mc) ! based on 5MC1 patch ! 3/16/2005 p. o'donoghue RESI 5MC -1.00 ATOM P P 1.50 ! ATOM O1P ON3 -0.78 ! H42 H41 ATOM O2P ON3 -0.78 ! \ / ATOM O5' ON2 -0.57 ! H51 N4 ATOM C5' CN8B -0.08 ! | | ATOM H5' HN8 0.09 ! H52-C5M C4 ATOM H5'' HN8 0.09 ! | \ / \\ GROUP ! H53 C5 N3 ATOM C4' CN7 0.16 ! || | ATOM H4' HN7 0.09 ! H6-C6 C2 ATOM O4' ON6B -0.50 ! \ / \\ ATOM C1' CN7B 0.16 ! N1 O2 ATOM H1' HN7 0.09 ! \ GROUP ! \ ATOM N1 NN2 -0.13 ! \ ATOM C6 CN3 0.05 ! O1P H5' H4' O4' \ ATOM H6 HN3 0.17 ! | | \ / \ \ ATOM C5 CN3D -0.11 ! -P-O5'-C5'---C4' C1' ATOM C5M CN9 -0.22 ! | | \ / \ ATOM H51 HN9 0.09 ! O2P H5'' C3'--C2' H1' ATOM H52 HN9 0.09 ! / \ / \ ATOM H53 HN9 0.09 ! O3' H3' O2' H2'' ATOM C2 CN1 0.52 ! | | ATOM O2 ON1C -0.49 ! H2' ATOM N3 NN3 -0.66 ATOM C4 CN2 0.65 ATOM N4 NN1 -0.75 ATOM H41 HN1 0.37 ATOM H42 HN1 0.33 GROUP ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 BOND C2 N3 C4 N4 N4 H41 N4 H42 BOND C4 C5 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C6 H6 BOND C5 C5M C5M H51 C5M H52 C5M H53 DOUBLE C2 O2 C5 C6 N3 C4 IMPR C2 N1 N3 O2 C4 N3 C5 N4 IMPR N4 C4 H41 H42 DONO H42 N4 DONO H2' O2' DONO H41 N4 ACCE O2 C2 ACCE N3 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' !Topology file for MIA !made by Anurag Sethi MASS 199 HE1M 1.00800 H ! for alkene; RHC=CR MASS 200 HAM 1.00800 H ! Anal.ogy with HA MASS 201 HNAM 1.00800 H ! Aliphatic H MASS 202 HM 1.00800 H ! Aliphatic H MASS 203 HN1M 1.00800 H ! Analogy with HN1 MASS 204 HN3M 1.00800 H ! Analogy with HN3 MASS 205 CNTM 12.01100 C ! dimethylamine methyl carbon MASS 206 CN5M 12.01100 C ! Analogy with CN5 MASS 207 CN4M 12.01100 C ! Analogy with CN4 MASS 208 CN2M 12.01100 C ! Analogy with CN2 MASS 209 CT3M 12.01100 C ! Analogy with CT3 MASS 210 CE0M 12.01100 C ! Analogy with CE0 MASS 211 CE1M 12.01100 C ! Analogy with CE1 MASS 212 NN2M 14.00700 N ! Analogy with NN2 MASS 213 NN3M 14.00700 N ! Analogy with NN3A MASS 214 NN4M 14.00700 N ! Analogy with NN4 MASS 215 NN1M 14.00700 N ! Analogy with NN2 MASS 216 SM 32.06000 S ! sulphur !H153 H151 H122 ! \ | | RESI MIA -1.00 ! C15 H121-C12 H6! ATOM P P 1.50 ! / \ / \ / ATOM O1P ON3 -0.78 ! H152 C14==C13 N6 ATOM O2P ON3 -0.78 ! / | | ATOM O5' ON2 -0.57 ! H161-C16 H13 C6 ATOM C5' CN8B -0.08 ! /| // \ ATOM H5' HN8 0.09 ! /H163 H113 N1 C5--N7\\ ATOM H5'' HN8 0.09 ! H162 | | || C8-H8 GROUP ! H112-C11 C2 C4--N9/ ATOM C4' CN7 0.16 ! / \ / \\ / \ ATOM H4' HN7 0.09 ! H111 S10 N3 \ ATOM O4' ON6B -0.50 ! \ ATOM C1' CN7B 0.16 ! \ ATOM H1' HN7 0.09 ! \ GROUP ! O1P H5' H4' O4' \ ATOM N9 NN2M -0.05 ! | | \ / \ \ ATOM C5 CN5M 0.28 ! -P-O5'-C5'---C4' C1' ATOM N7 NN4M -0.71 ! | | \ / \ ATOM C8 CN4M 0.34 ! O2P H5'' C3'--C2' H1' ATOM H8 HN3M 0.12 ! / \ / \ ATOM N1 NN3M -0.74 ! O3' H3' O2' H2'' ATOM C2 CN4M 0.63 ! | | ATOM S10 SM -0.05 ! H2' ATOM C11 CT3M -0.22 ATOM H111 HAM 0.09 ATOM H112 HAM 0.09 ATOM H113 HAM 0.09 ATOM N3 NN3M -0.75 ATOM C4 CN5M 0.43 ATOM C6 CN2M 0.46 ATOM N6 NN1M -0.51 ATOM H6 HN1M 0.38 ATOM C12 CNTM -0.06 ATOM H121 HNAM 0.09 ATOM H122 HNAM 0.09 ATOM C13 CE1M -0.15 ATOM H13 HE1M 0.15 ATOM C14 CE0M -0.10 ATOM C15 CT3M -0.22 ATOM H151 HM 0.09 ATOM H152 HM 0.09 ATOM H153 HM 0.09 ATOM C16 CT3M -0.22 ATOM H161 HM 0.09 ATOM H162 HM 0.09 ATOM H163 HM 0.09 GROUP ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N1 C6 N6 BOND N6 H6 N6 C12 C6 C5 C5 N7 BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2 S10 BOND S10 C11 C11 H111 C11 H112 C11 H113 BOND C12 H121 C12 H122 C12 C13 C13 H13 BOND C14 C15 C14 C16 C15 H151 C15 H152 BOND C15 H153 C16 H161 C16 H162 C16 H163 DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 DOUBLE C13 C14 IMPR N6 C6 H6 C12 C6 N1 C5 N6 DONO H6 N6 DONO H2' O2' ACCE N3 ACCE N7 ACCE N1 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5'