!=========================================================================
! 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