REMARKS toptrnah topology append file for TRNA REMARKS use with TOPNAH1*, PARNAH1* set echo=false end autogenerate angles=false dihedrals=false end ! NOTE: NO DONORS OR ACCEPTORS FOR TIPS ! PATCHES TO BE APPENDED TO TOPRNA5 MAKING IT TOPTRNA5 ! All the modified nucleotides in tRNA are implemented ! as patches ('TYPE II'). ! ------------ work in progress ---------------------- ! /LN ! ! No additional atomtypes seem to be necessary ! !!!! ****>>>>CHARGES NEED CHECKING (and atomtypes too) ! SUBDIVISIONS ARE STILL MISSING ! !----------------------------------------------------------- ! PRESidue DHU ! Make Dihydro-U out of U ! === GROUP MODIFY ATOM C5 TYPE=C2 CHARge=-0.07 END ADD ATOM H51 TYPE=H CHARge=0.035 END ADD ATOM H52 TYPE=H CHARge=0.035 END DELETE ATOM H5 END !! Lennart left this out GROUP MODIFY ATOM C6 TYPE=C2 CHARge=-0.07 END ADD ATOM H61 TYPE=H CHARge=0.035 END ADD ATOM H62 TYPE=H CHARge=0.035 END DELETE ATOM H6 END !! Lennart left this out ADD BOND C5 H51 ADD BOND C5 H52 ADD BOND C6 H61 ADD BOND C6 H62 ADD ANGLE C4 C5 H51 ADD ANGLE C4 C5 H52 ADD ANGLE C6 C5 H51 ADD ANGLE C6 C5 H52 ADD ANGLE H51 C5 H52 ADD ANGLE C5 C6 H61 ADD ANGLE C5 C6 H62 ADD ANGLE N1 C6 H61 ADD ANGLE N1 C6 H62 ADD ANGLE H61 C6 H62 DELE IMPROPER N1 C2 N3 C4 ! The ring is no longer aromatic DELE IMPROPER C2 N3 C4 C5 DELE IMPROPER N3 C4 C5 C6 DELE IMPROPER C4 C5 C6 N1 DELE IMPROPER C5 C6 N1 C2 DELE IMPROPER C6 N1 C2 N3 ADD DIHE N1 C2 N3 C4 ! So we use plain dihedrals instead ADD DIHE C2 N3 C4 C5 ADD DIHE N3 C4 C5 C6 ADD DIHE C4 C5 C6 N1 ADD DIHE C5 C6 N1 C2 ADD DIHE C6 N1 C2 N3 ! NO DIHEDRALS FOR OUR NEW HYDROGEN FRIENDS (YET) END {DHU} !----------------------------------------------------------------------------- PRESidue 7MG ! 7-Methyl guanosine ****>>> NOTE: Is charged at pH 7 ! === chemistry unclear (CANTOR&SCHIMMEL have charged O) MODIFY ATOM C5 TYPE=CB CHARGE=0.15 END MODIFY ATOM C8 TYPE=CE CHARGE=0.25 END GROUP MODIFY ATOM N7 TYPE=NB CHARGE=-0.15 END! Type? All these charges are guesswork ADD ATOM C7 TYPE=C3 CHARGE=0.045 END ADD ATOM H71 TYPE=H CHARGE=0.035 END ADD ATOM H72 TYPE=H CHARGE=0.035 END ADD ATOM H73 TYPE=H CHARGE=0.035 END ADD BOND N7 C7 ADD BOND C7 H71 ADD BOND C7 H72 ADD BOND C7 H73 ADD ANGLE C5 N7 C7 ADD ANGLE C8 N7 C7 ADD ANGLE N7 C7 H71 ADD ANGLE N7 C7 H72 ADD ANGLE N7 C7 H73 ADD ANGLE H71 C7 H72 ADD ANGLE H71 C7 H73 ADD ANGLE H72 C7 H73 ADD IMPROPER C7 C5 C8 N7 ADD DIHEDRAL C8 N7 C7 H71 ADD DIHEDRAL C8 N7 C7 H72 ADD DIHEDRAL C8 N7 C7 H73 ADD IC C5 C8 *N7 C7 1.378 000.00 -180.00 000.00 0.000 END {7MG} !-------------------------------------------------------------- PRESidue 2M2G ! N2-Dimethyl guanosine ! ==== DELETE ATOM H21 END DELETE ATOM H22 END GROUP MODIFY ATOM N2 TYPE=N2 CHARGE=-0.42 END ADD ATOM C2A TYPE=C3 CHARGE=0.105 END! Just replace the Hs with methyls ADD ATOM H2A1 TYPE=H CHARGE=0.035 END ADD ATOM H2A2 TYPE=H CHARGE=0.035 END ADD ATOM H2A3 TYPE=H CHARGE=0.035 END ADD ATOM C2B TYPE=C3 CHARGE=0.105 END ADD ATOM H2B1 TYPE=H CHARGE=0.035 END ADD ATOM H2B2 TYPE=H CHARGE=0.035 END ADD ATOM H2B3 TYPE=H CHARGE=0.035 END ADD BOND N2 C2B ADD BOND N2 C2A ADD BOND C2A H2A1 ADD BOND C2A H2A2 ADD BOND C2A H2A3 ADD BOND C2B H2B1 ADD BOND C2B H2B2 ADD BOND C2B H2B3 ADD ANGLE C2 N2 C2B ADD ANGLE C2 N2 C2A ADD ANGLE C2B N2 C2A ADD ANGLE N2 C2A H2A1 ADD ANGLE N2 C2A H2A2 ADD ANGLE N2 C2A H2A3 ADD ANGLE H2A1 C2A H2A2 ADD ANGLE H2A1 C2A H2A2 ADD ANGLE H2A2 C2A H2A3 ADD ANGLE N2 C2B H2B1 ADD ANGLE N2 C2B H2B2 ADD ANGLE N2 C2B H2B3 ADD ANGLE H2B1 C2B H2B2 ADD ANGLE H2B1 C2B H2B2 ADD ANGLE H2B2 C2B H2B3 ADD DIHEDRAL N3 C2 N2 C2B ADD DIHEDRAL C2 N2 C2A H2A1 ADD DIHEDRAL C2 N2 C2A H2A2 ADD DIHEDRAL C2 N2 C2A H2A3 ADD DIHEDRAL C2 N2 C2B H2B1 ADD DIHEDRAL C2 N2 C2B H2B2 ADD DIHEDRAL C2 N2 C2B H2B3 ADD IMPROPER C2A C2B C2 N2 ADD IC N3 C2 N2 C2B 1.3310 120.68 179.25 127.00 0.00 ADD IC C2B C2 *N2 C2A 0.00 127.00 -178.12 116.53 0.00 END {2M2G} !-------------------------------------------------------------- PRES M2G ! N2-Methyl guanosine ! === DELEte ATOM H22 END GROUP MODIFY ATOM N2 TYPE=N2 CHARGE=-0.42 END MODIFY ATOM H21 TYPE=H2 CHARGE=0.21 END ADD ATOM C2A TYPE=C3 CHARGE=0.105 END! Just replace the H with a methyl ADD ATOM H2A1 TYPE=H CHARGE=0.035 END ADD ATOM H2A2 TYPE=H CHARGE=0.035 END ADD ATOM H2A3 TYPE=H CHARGE=0.035 END ADD BOND N2 C2A ADD BOND C2A H2A1 ADD BOND C2A H2A2 ADD BOND C2A H2A3 ADD ANGLE N2 C2A H2A1 ADD ANGLE N2 C2A H2A2 ADD ANGLE N2 C2A H2A3 ADD ANGLE H2A1 C2A H2A2 ADD ANGLE H2A1 C2A H2A2 ADD ANGLE H2A2 C2A H2A3 ADD ANGLE C2 N2 C2A ADD ANGLE H21 N2 C2A ADD IMPROPER C2A H21 C2 N2 ADD DIHEDRAL C2 N2 C2A H2A1 ADD DIHEDRAL C2 N2 C2A H2A2 ADD DIHEDRAL C2 N2 C2A H2A3 ADD IC H21 C2 *N2 C2A 0.00 127.00 -178.12 116.53 0.00 END {M2G} !-------------------------------------------------------------- PRESidue 2'OM ! 2'O-Methyl, to be applied to any nucleotide ! ==== DELEte ATOM H2' END GROUP MODIFY ATOM O2' TYPE=OS CHARGE=-0.30 END ADD ATOM C2A TYPE=C3 CHARGE=0.195 END ADD ATOM H21' TYPE=H CHARGE=0.035 END ADD ATOM H22' TYPE=H CHARGE=0.035 END ADD ATOM H23' TYPE=H CHARGE=0.035 END ADD BOND O2' C2A ADD BOND C2A H21' ADD BOND C2A H22' ADD BOND C2A H23' ADD ANGLE C2' O2' C2A ADD ANGLE O2' C2A H21' ADD ANGLE O2' C2A H22' ADD ANGLE O2' C2A H23' ADD ANGLE H21' C2A H22' ADD ANGLE H21' C2A H23' ADD ANGLE H22' C2A H23' ADD DIHEDRAL C2' O2' C2A H21' ADD DIHEDRAL C2' O2' C2A H22' ADD DIHEDRAL C2' O2' C2A H23' ADD DIHEDRAL C3' C2' O2' C2A ADD IC C2A O2' C2' C3' 1.45 114.97 148.63 11.92 1.5284 END {2'OM} !--------------------------------------------------------------- PRESidue PSI ! Pseudouridine; U with ribose at C5, not N1 ! === DELE BOND C1' N1 DELE ANGLE O4' C1' N1 DELE ANGLE N1 C1' C2' DELE ANGLE C1' N1 C2 DELE ANGLE C1' N1 C6 DELE DIHEDRAL O4' C1' N1 C2 !! DELE IMPROPER N1 C2' O4' C1' !! typo in Lennart's file DELE IMPROPER C1' C2 C6 N1 DELE IC C1' C2 *N1 C6 DELE IC C3' C2' C1' N1 DELE ATOM H5 END MODIFY ATOM C5 TYPE=CS CHARGE=0.00 END ! Just make this another kind of C MODIFY ATOM C6 TYPE=CF CHARGE=0.165 EXCLUSION=( N3 ) END MODIFY ATOM H6 TYPE=H CHARGE=0.035 END GROUP MODIFY ATOM N1 TYPE=NA CHARGE=-0.30 EXCLUSION=( C4 ) END ADD ATOM H11 TYPE=H CHARGE=0.10 END ADD BOND C1' C5 ADD BOND N1 H11 ADD ANGLE O4' C1' C5 ADD ANGLE C5 C1' C2' ADD ANGLE C1' C5 C4 ADD ANGLE C1' C5 C6 ADD ANGLE C2 N1 H11 ADD ANGLE C6 N1 H11 ADD DIHEDRAL O4' C1' C5 C6 ADD IMPROPER C5 C2' O4' C1' ADD IMPROPER C1' C6 C4 C5 ADD IMPROPER H11 C2 C6 N1 ADD IC C4 C5 C6 N1 0.0000 000.00 000.00 000.00 0.000 ADD IC C3' C2' C1' C5 1.5284 101.97 144.39 113.71 1.500 ADD IC C2' C1' C5 C6 1.5215 113.71 144.99 121.63 1.36 ADD IC C1' C6 *C5 C4 1.5000 121.60 180.00 121.60 1.44 ADD IC H11 C2 *N1 C6 1.0900 117.06 180.00 122.08 1.37 END {PSI} !--------------------------------------------------------------- PRESidue 5MC ! 5-Methyl cytosine ! === !Inference from THY(=5MU): DELE ATOM H5 END GROUP MODIFY ATOM C5 TYPE=CS CHARGE=0.00 END ADD ATOM C5A TYPE=C3 CHARGE=-0.105 END ADD ATOM H51 TYPE=H CHARGE=0.035 END ADD ATOM H52 TYPE=H CHARGE=0.035 END ADD ATOM H53 TYPE=H CHARGE=0.035 END ADD BOND C5 C5A ADD BOND C5A H51 ADD BOND C5A H52 ADD BOND C5A H53 ADD ANGLE C4 C5 C5A ADD ANGLE C5A C5 C6 ADD ANGLE C5 C5A H51 ADD ANGLE C5 C5A H52 ADD ANGLE C5 C5A H53 ADD ANGLE H52 C5A H51 ADD ANGLE H53 C5A H52 ADD ANGLE H51 C5A H53 ADD DIHEDRAL C6 C5 C5A H51 ADD DIHEDRAL C6 C5 C5A H52 ADD DIHEDRAL C6 C5 C5A H53 ADD IMPROPER C5A C4 C6 C5 ADD IC C4 C6 *C5 C5A 1.4439 120.78 -179.94 121.63 1.5000 END {5MC} !----------------------------------------------------------------- PRESidue 1MA ! 1-Methyl adenine; (chemistry unclear) ! === DELE ACCE N1 GROUP MODIFY ATOM N1 TYPE=NA CHARGE=-0.25 EXCL=( C4 ) END ADD ATOM C1 TYPE=C3 CHARGE=-0.005 END ADD ATOM H11 TYPE=H CHARGE=0.035 END ADD ATOM H12 TYPE=H CHARGE=0.035 END ADD ATOM H13 TYPE=H CHARGE=0.035 END GROUP MODIFY ATOM C6 TYPE=CH CHARGE=0.115 EXCL=( N3 ) END! Probably a CH ADD ATOM H6 TYPE=H CHARGE=0.035 END ADD BOND N1 C1 ADD BOND C6 H6 ADD BOND C1 H11 ADD BOND C1 H12 ADD BOND C1 H13 ADD ANGLE C6 N1 C1 ADD ANGLE C2 N1 C1 ADD ANGLE N6 C6 H6 ADD ANGLE N1 C6 H6 ADD ANGLE C5 C6 H6 ADD ANGLE N1 C1 H11 ADD ANGLE N1 C1 H12 ADD ANGLE N1 C1 H13 ADD ANGLE H12 C1 H11 ADD ANGLE H13 C1 H12 ADD ANGLE H11 C1 H13 ADD DIHEDRAL C2 N1 C1 H11 ADD DIHEDRAL C2 N1 C1 H12 ADD DIHEDRAL C2 N1 C1 H13 ADD IMPROPER C1 C2 C6 N1 ADD IC C6 C2 *N1 C1 1.4021 125.24 180.00 117.40 1.49 END {1MA} !-------------------------------------------------------------- PRESidue WYE ! Y-base (wyebutosine) as a patch to GUA ! === Atom numbers according to TRNAMIT.BHV DELE ACCE N3 END DELE ATOM H1 END DELE ATOM H21 END DELE ATOM H22 END GROUP MODIFY ATOM N3 TYPE=NA CHARGE=-0.20 EXCL=( C6 ) END ADD ATOM C3 TYPE=C3 CHARGE=-0.005 END ADD ATOM H31 TYPE=H CHARGE=0.035 END ADD ATOM H32 TYPE=H CHARGE=0.035 END ADD ATOM H33 TYPE=H CHARGE=0.035 END GROUP MODIFY ATOM N1 TYPE=NA CHARGE=-0.25 EXCL= ( C4 ) END ADD ATOM C11 TYPE=CA CHARGE=0.10 END ADD ATOM C10 TYPE=C3 CHARGE=-0.005 END ADD ATOM H101 TYPE=H CHARGE=0.035 END ADD ATOM H102 TYPE=H CHARGE=0.035 END ADD ATOM H103 TYPE=H CHARGE=0.035 END ADD ATOM C12 TYPE=CA CHARGE=0.05 END GROUP MODIFY ATOM C2 TYPE=CB CHARGE=0.35 EXCL=( C5 ) END MODIFY ATOM N2 TYPE=NB CHARGE=-0.25 END ADD ATOM C13 TYPE=C2 CHARGE=-0.07 END ADD ATOM H131 TYPE=H CHARGE=0.035 END ADD ATOM H132 TYPE=H CHARGE=0.035 END ADD ATOM C14 TYPE=C2 CHARGE=-0.07 END ADD ATOM H141 TYPE=H CHARGE=0.035 END ADD ATOM H142 TYPE=H CHARGE=0.035 END ADD ATOM C15 TYPE=CH CHARGE=-0.035 END ADD ATOM H15 TYPE=H CHARGE=0.035 END ADD ATOM C16 TYPE=C CHARGE=0.30 END! ? ADD ATOM O18 TYPE=OS CHARGE=-0.20 END ADD ATOM C19 TYPE=C3 CHARGE=-0.005 END ADD ATOM H191 TYPE=H CHARGE=0.035 END ADD ATOM H192 TYPE=H CHARGE=0.035 END ADD ATOM H193 TYPE=H CHARGE=0.035 END ADD ATOM O17 TYPE=O CHARGE=-0.20 END ADD ATOM N20 TYPE=NA CHARGE=-0.26 END ADD ATOM H20 TYPE=H CHARGE=0.26 END ADD ATOM C21 TYPE=C CHARGE=0.30 END ADD ATOM O23 TYPE=O CHARGE=-0.20 END ADD ATOM O22 TYPE=OS CHARGE=-0.20 END ADD ATOM C24 TYPE=C3 CHARGE=-0.005 END ADD ATOM H241 TYPE=H CHARGE=0.035 END ADD ATOM H242 TYPE=H CHARGE=0.035 END ADD ATOM H243 TYPE=H CHARGE=0.035 END ADD BOND N1 C12 ADD BOND C12 C11 ADD BOND C11 C10 ADD BOND C11 N2 ADD BOND N3 C3 ADD BOND N20 H20 ADD BOND C12 C13 ADD BOND C13 C14 ADD BOND C14 C15 ADD BOND C15 C16 ADD BOND C16 O17 ADD BOND C16 O18 ADD BOND O18 C19 ADD BOND C15 N20 ADD BOND N20 C21 ADD BOND C21 O23 ADD BOND C21 O22 ADD BOND O22 C24 ADD BOND C3 H31 ADD BOND C3 H32 ADD BOND C3 H33 ADD BOND C10 H101 ADD BOND C10 H102 ADD BOND C10 H103 ADD BOND C13 H131 ADD BOND C13 H132 ADD BOND C14 H141 ADD BOND C14 H142 ADD BOND C15 H15 ADD BOND C19 H191 ADD BOND C19 H192 ADD BOND C19 H193 ADD BOND C24 H241 ADD BOND C24 H242 ADD BOND C24 H193 ADD ANGLE C6 N1 C12 ADD ANGLE C12 N1 C2 ADD ANGLE C2 N3 C3 ADD ANGLE C4 N3 C3 ADD ANGLE C2 N2 C11 ADD ANGLE N2 C11 C10 ADD ANGLE N2 C11 C12 ADD ANGLE C10 C11 C12 ADD ANGLE N1 C12 C13 ADD ANGLE C11 C12 C13 ADD ANGLE C12 C13 C14 ADD ANGLE C13 C14 C15 ADD ANGLE C14 C15 N20 ADD ANGLE C14 C15 C16 ADD ANGLE C15 C16 O17 ADD ANGLE C15 C16 O18 ADD ANGLE C15 N20 H20 ADD ANGLE C15 N20 C21 ADD ANGLE C16 O18 C19 ADD ANGLE H20 N20 C21 ADD ANGLE N20 C21 O23 ADD ANGLE N20 C21 O22 ADD ANGLE O23 C21 O22 ADD ANGLE C21 O22 C24 ADD ANGLE N3 C3 H31 ADD ANGLE N3 C3 H32 ADD ANGLE N3 C3 H33 ADD ANGLE H32 C3 H31 ADD ANGLE H33 C3 H32 ADD ANGLE H31 C3 H33 ADD ANGLE C11 C10 H101 ADD ANGLE C11 C10 H102 ADD ANGLE C11 C10 H103 ADD ANGLE H102 C10 H101 ADD ANGLE H103 C10 H102 ADD ANGLE H101 C10 H103 ADD ANGLE O18 C19 H191 ADD ANGLE O18 C19 H192 ADD ANGLE O18 C19 H193 ADD ANGLE H192 C19 H191 ADD ANGLE H193 C19 H192 ADD ANGLE H191 C19 H193 ADD ANGLE O22 C24 H241 ADD ANGLE O22 C24 H242 ADD ANGLE O22 C24 H243 ADD ANGLE H242 C24 H241 ADD ANGLE H243 C24 H242 ADD ANGLE H241 C24 H243 ADD ANGLE C12 C13 H131 ADD ANGLE C12 C13 H132 ADD ANGLE C14 C13 H131 ADD ANGLE C14 C13 H132 ADD ANGLE H131 C13 H132 ADD ANGLE C13 C14 H141 ADD ANGLE C13 C14 H142 ADD ANGLE C15 C14 H141 ADD ANGLE C15 C14 H142 ADD ANGLE H141 C14 H142 ADD ANGLE C14 C15 H15 ADD ANGLE C16 C15 H15 ADD ANGLE N20 C15 H15 ADD DIHEDRAL C2 N3 C3 H31 ADD DIHEDRAL C2 N3 C3 H32 ADD DIHEDRAL C2 N3 C3 H33 ADD DIHEDRAL C12 C11 C10 H101 ADD DIHEDRAL C12 C11 C10 H102 ADD DIHEDRAL C12 C11 C10 H103 ADD DIHEDRAL C16 O18 C19 H191 !!typo in Lennart's file ADD DIHEDRAL C16 O18 C19 H192 !! ADD DIHEDRAL C16 O18 C19 H193 !! ADD DIHEDRAL C21 O22 C24 H241 ADD DIHEDRAL C21 O22 C24 H242 ADD DIHEDRAL C21 O22 C24 H243 ! Special ADD DIHEDRALs to keep extra ring parallel. Cf Trp in PARAM7 ADD DIHEDRAL C11 C2 N1 C5 ADD DIHEDRAL C11 N1 C2 C4 ADD DIHEDRAL N3 C2 N1 C12 ADD DIHEDRAL C6 N1 C2 N2 ADD DIHEDRAL N1 C12 C13 C14 ADD DIHEDRAL C12 C13 C14 C15 ! The protuberance ADD DIHEDRAL C13 C14 C15 C16 ADD DIHEDRAL C14 C15 C16 O18 ADD DIHEDRAL C15 C16 O18 C19 ADD DIHEDRAL C15 N20 C21 O22 ADD DIHEDRAL C14 C15 N20 C21 ADD DIHEDRAL C15 N20 C21 O22 ADD DIHEDRAL N20 C21 O22 C24 ADD IMPROPER C14 C16 N20 C15 ADD IMPROPER H20 C15 C21 N20 ADD IMPROPER O17 C15 O18 C16 ADD IMPROPER O23 O22 N20 C21 ADD IMPROPER C3 C4 C2 N3 ! The methyl at N3 ADD IMPROPER C12 N1 C2 N2 ! The extra ring ADD IMPROPER C11 C12 N1 C2 ADD IMPROPER N2 C11 C12 N1 ADD IMPROPER C2 N2 C11 C12 ADD IMPROPER C11 N2 C2 N1 ADD IMPROPER C10 N2 C12 C11 ADD IMPROPER C13 N1 C11 C12 ! Start of protuberance ADD DONO H20 N20 ADD ACCE O17 C16 ADD ACCE O23 C21 ! IC-table is to be filled from parameters and/or crystal coordinates ! The torsion angles are mostly guesswork so use --- " --- ADD IC C2 C4 *N3 C3 0.0000 000.00 180.00 000.00 0.0000 ADD IC C12 N2 *C11 C10 0.0000 000.00 180.00 000.00 0.0000 ADD IC C6 C2 *N1 C12 0.0000 000.00 180.00 000.00 0.0000 ADD IC C2 N1 C12 C11 0.0000 000.00 0.00 000.00 0.0000 ADD IC C6 N1 C12 C13 0.0000 000.00 0.00 000.00 0.0000 ADD IC N1 C12 C13 C14 0.0000 000.00 180.00 000.00 0.0000 ADD IC C12 C13 C14 C15 0.0000 000.00 180.00 000.00 0.0000 ADD IC C13 C14 C15 C16 0.0000 000.00 60.00 000.00 0.0000 ADD IC C13 C14 C15 N20 0.0000 000.00 -60.00 000.00 0.0000 ADD IC C14 C15 C16 O18 0.0000 000.00 180.00 000.00 0.0000 ADD IC C15 C16 O18 C19 0.0000 000.00 180.00 000.00 0.0000 ADD IC O18 C15 *C16 O17 0.0000 000.00 180.00 000.00 0.0000 ADD IC C14 C15 N20 C21 0.0000 000.00 0.00 000.00 0.0000 ADD IC C15 N20 C21 O22 0.0000 000.00 0.00 000.00 0.0000 ADD IC N20 C21 O22 C24 0.0000 000.00 180.00 000.00 0.0000 ADD IC C21 C15 *N20 H20 0.0000 000.00 180.00 000.00 0.0000 ADD IC O22 N20 *C21 O23 0.0000 000.00 180.00 000.00 0.0000 END {WYE} !-------------------------------------------------------------- PRESidue 2AMP ! 2-AMP patch to ADE. Move NH2 from C6 to C2 ! ==== DELE ATOM N6 END DELE ATOM H61 END DELE ATOM H62 END MODIFY ATOM C6 TYPE=CE CHARGE=0.26 END GROUP MODIFY ATOM C2 TYPE=CA CHARGE=0.28 END ADD ATOM N2 TYPE=N2 CHARGE=-0.42 END ADD ATOM H21 TYPE=H2 CHARGE=0.21 END ADD ATOM H22 TYPE=H2 CHARGE=0.21 END ADD BOND C2 N2 ADD BOND N2 H21 !!! typo in Lennart's file ADD BOND N2 H22 ADD ANGLE N1 C2 N2 ADD ANGLE N3 C2 N2 ADD ANGLE C2 N2 H21 ADD ANGLE C2 N2 H22 ADD ANGLE H21 N2 H22 ADD DIHEDRAL N1 C2 N2 H21 ADD IMPROPER H22 C2 H21 N2 ADD IMPROPER N2 N3 N1 C2 ADD DONOR H21 N2 ADD DONOR H22 N2 ADD IC N1 N3 *C2 N2 0.0000 000.00 180.00 000.00 0.0000 ADD IC N3 C2 N2 H21 0.0000 000.00 180.00 000.00 0.0000 ADD IC H21 C2 *N2 H22 0.0000 000.00 180.00 000.00 0.0000 END {2AMP} !-------------------------------------------------------------- set echo=true end