!========================================================================= ! CHARMM topology for SAM !========================================================================= RESI SAM 1.00 ! S-adenosyl methionine GROUP ! Built by merging ADE with the patch for ATOM C4' CN7 0.16 ! SAHC (S-adenosyl homocysteine) obtained from ATOM H4' HN7 0.09 ! Alex MacKerell ATOM O4' ON6B -0.50 ! ATOM C1' CN7B 0.16 ! ATOM H1' HN7 0.09 ! H61 H62 GROUP ! \ / ATOM N9 NN2 -0.05 ! N6 ATOM C5 CN5 0.28 ! | ATOM N7 NN4 -0.71 ! C6 ATOM C8 CN4 0.34 ! // \ ATOM H8 HN3 0.12 ! N1 C5--N7\\ ATOM N1 NN3A -0.74 ! | || C8-H8 ATOM C2 CN4 0.50 ! C2 C4--N9/ ATOM H2 HN3 0.13 ! / \\ / \ ATOM N3 NN3A -0.75 ! H2 N3 \ ATOM C4 CN5 0.43 ! ATOM C6 CN2 0.46 ! ATOM N6 NN1 -0.77 ! ATOM H61 HN1 0.38 ! ATOM H62 HN1 0.38 ! GROUP ! ATOM C2' CN7B 0.14 ! ATOM H2'' HN7 0.09 ! ATOM O2' ON5 -0.66 ! ATOM H2' HN5 0.43 ! !From SAHC patch GROUP ATOM N NH3 -0.30 ! ATOM HT1 HC 0.33 ! (2) HT1 ATOM HT2 HC 0.33 ! | / ATOM HT3 HC 0.33 !(1)--CA--N--HT2 (+) ATOM CA CT1 0.21 ! | \ ATOM HA HB 0.10 ! HA HT3 GROUP ! ATOM CB CT2 -0.18 ! HE2 (+) ATOM HB1 HA 0.09 ! | ATOM HB2 HA 0.09 ! HE1--CE--HE3 GROUP ! | ATOM CG CT2 -0.20 !hms -0.14 HB1 HG1 | H5' H4' O4' Ade ATOM HG1 HA 0.20 !hms 0.09 | | | | \ / \ / ATOM HG2 HA 0.20 !hms 0.09 (1)--CB--CG--SD--C5'----C4' C1'-H1' ATOM SD S 0.40 !hms -0.09 | | | | | ATOM C5' CN8B -0.20 !hms -0.13 HB2 HG2 H5'' H3'-C3'--C2'-H2'' ATOM H5' HN8 0.20 !hms 0.09 | | ATOM H5'' HN8 0.20 !hms 0.09 H3T--O3' O2'-H2' ATOM CE CT3 -0.40 !hms ATOM HE1 HA 0.20 !hms ATOM HE2 HA 0.20 !hms ATOM HE3 HA 0.20 !hms GROUP ATOM C3' CN7 0.14 ATOM H3' HN7 0.09 ATOM O3' ON5 -0.66 ATOM H3T HN5 0.43 GROUP ! OT2(-) ATOM C CC 0.34 ! / ATOM OT1 OC -0.67 ! (2)-C ATOM OT2 OC -0.67 ! \\ ! OT1 ! BOND 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 H61 N6 H62 C6 C5 C5 N7 BOND C2' C3' C2' O2' O2' H2' C3' O3' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2 H2 DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 IMPR N6 C6 H61 H62 C6 N1 C5 N6 !From SAHC patch DOUB C OT1 BOND N CA O3' H3T BOND CB CA CG CB SD CG C5' SD C CA BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 BOND HT1 N HT2 N HT3 N OT2 C IMPR OT1 CA OT2 C !hms BOND CE HE1 CE HE2 CE HE3 CE SD ! DONO H61 N6 DONO H62 N6 DONO H2' O2' ACCE N3 ACCE N7 ACCE N1 ACCE O2' ACCE O3' ACCE O4' !From SAHC patch DONOR HT1 N DONOR HT2 N DONOR HT3 N ACCEPTOR OT1 C ACCEPTOR OT2 C !hms DONOR H3T O3' ! PATCHING FIRST NONE LAST NONE !========================================================================= ! CHARMM topology for F- !========================================================================= ! Mass entry !------------------------------------------------------------------------- MASS 200 FLA 18.998403 F ! Fluoride ion !------------------------------------------------------------------------- ! Residue !------------------------------------------------------------------------- RESI FLA -1.00 ! Fluoride ion GROUP ATOM FLA FLA -1.00 PATCHING FIRST NONE LAST NONE