Br  C      1.98000  300.00000
Br  CA     1.87000  300.00000     wlj
Br  CM     1.90000  300.00000     wlj
Br  CT     1.94500  245.00000     wlj
Br  CZ     1.78400  330.00000     wlj
Br  DM     0.30000  300.00000     wlj
Br  Si     2.19000  151.00000     wlj
C   C      1.51000  350.00000     wlj oxalic acid, etc.
C   C!     1.46000  385.00000     wlj
C   C2     1.52200  317.00000     GLY,ASP,GLU
C   C3     1.52200  317.00000     END
C   C=     1.46000  385.00000     wlj acrolein
C   CA     1.49000  400.00000     wlj 8/97
C   CB     1.41900  447.00000     GUA
C   CD     1.40000  469.00000     TYR
C   CH     1.52200  317.00000     AA
C   CJ     1.44400  410.00000     URA
C   CM     1.44400  410.00000     THY
C   CT     1.52200  317.00000
C   CW     1.49000  400.00000     bhap,                   copy from C -CA         rcr HIVRT
C   Cl     1.79000  300.00000     wlj
C   F      1.35700  420.00000     wlj
C   HC     1.09000  340.00000     wlj 7/96
C   N      1.33500  490.00000     AA
C   N*     1.38300  424.00000     CYT,URA
C   N=     1.29000  457.00000     imine
C   NA     1.38800  418.00000     URAGUA
C   NC     1.35800  457.00000     CYT
C   NM     1.33500  490.00000     AA
C   NT     1.52200  317.00000     nev,                    copy from C -CT         rcr HIVRT
C   O      1.22900  570.00000     URAGUA,CYT,AA
C   O2     1.25000  656.00000     GLU,ASP
C   OH     1.36400  450.00000     TYR
C   OS     1.32700  214.00000     J.Comp.Chem.1990,11,1181 SKF8
C   S=     1.64000  400.00000     wlj thioamide, etc.
C!  C!     1.46000  385.00000     wlj
C!  CA     1.40000  469.00000
C!  CM     1.46000  385.00000     wlj
C!  CR     1.46000  385.00000     wlj
C!  CS     1.46000  385.00000     wlj
C!  CU     1.46000  385.00000     wlj
C!  CV     1.46000  385.00000     wlj
C!  CW     1.46000  385.00000     wlj
C!  NA     1.44000  385.00000     wlj
C!  NC     1.33900  483.00000     wlj
C$  CY     1.52200  317.00000     wj
C$  N$     1.33500  490.00000     wj
C$  O      1.22900  570.00000     wj
C*  C2     1.49500  317.00000     TRP(OL)
C*  CB     1.45900  388.00000     TRP
C*  CC     1.35200  546.00000     TRP
C*  CG     1.35200  546.00000     TRP
C*  CT     1.49500  317.00000     TRP(OL)
C*  CW     1.35200  546.00000     TRP
C*  HC     1.08000  340.00000
C+  CT     1.46000  532.80000     wlj - JACS 94, 4632 (1972)
C+  HC     1.08400  532.80000     wlj -      "
C2  C2     1.52600  260.00000     AA(OL)
C2  C3     1.52600  260.00000     ILE(OL)
C2  C7     1.50000  317.00000     OPLS hydrocarbons ff (jtr 5-14-91)
C2  C8     1.50000  317.00000     OPLS hydrocarbons ff (jtr 5-14-91)
C2  CA     1.51000  317.00000     PHE,TYR
C2  CC     1.50400  317.00000     HIS
C2  CD     1.51000  317.00000     PHE,TYR
C2  CH     1.52600  260.00000     AA,SUG
C2  CO     1.52600  260.00000     "
C2  CT     1.52600  260.00000     Added DSM (from C2-CH)
C2  F      1.38000  367.00000     wlj
C2  N      1.44900  337.00000     GLY(OL)
C2  N2     1.46300  337.00000     ARG(OL)
C2  N3     1.47100  367.00000     LYS(OL)
C2  NT     1.44800  382.00000     JACS 112, 8314 (90)
C2  OH     1.42500  386.00000     SUG(OL),SER
C2  OS     1.42500  320.00000     SUG(OL)
C2  S      1.81000  222.00000     CYX(OL)
C2  SH     1.81000  222.00000     CYS(OL)
C3  C3     1.52600  260.00000     Ethane
C3  C7     1.50000  317.00000     OPLS hydrocarbons ff (jtr 5-14-91)
C3  C8     1.50000  317.00000     OPLS hydrocarbons ff (jtr 5-14-91)
C3  CH     1.52600  260.00000     ALA
C3  CM     1.51000  317.00000     THY(use std C-C)
C3  CO     1.52600  260.00000     "
C3  CT     1.52600  260.00000     Added DSM (from C3-CH)
C3  N      1.44900  337.00000     TEST!!!!
C3  N*     1.47500  337.00000     9 methyl bases
C3  N2     1.46300  337.00000     ARG(OL)
C3  N3     1.47100  367.00000
C3  NT     1.44800  382.00000     "
C3  OH     1.42500  386.00000     SUG(OL),SER
C3  OS     1.42500  320.00000     DMP
C3  S      1.81000  222.00000     MET(OL)
C3  SH     1.81000  222.00000     CYS(OL)
C3  SY     1.81000  222.00000
C7  C7     1.34000  530.00000     OPLS hydrocarbons ff (jtr 5-14-91)
C7  C8     1.34000  530.00000     OPLS hydrocarbons ff (jtr 5-14-91)
C7  C9     1.34000  530.00000     OPLS hydrocarbons ff (jtr 5-14-91)
C7  CH     1.50000  317.00000     OPLS hydrocarbons ff (jtr 5-14-91)
C7  CT     1.50000  317.00000     OPLS hydrocarbons ff (jtr 5-14-91)
C8  C8     1.34000  530.00000     OPLS hydrocarbons ff (jtr 5-14-91)
C8  C9     1.34000  530.00000     OPLS hydrocarbons ff (jtr 5-14-91)
C8  CH     1.50000  317.00000     OPLS hydrocarbons ff (jtr 5-14-91)
C8  CT     1.50000  317.00000     OPLS hydrocarbons ff (jtr 5-14-91)
C8  SY     1.76000  222.00000
C9  C9     1.34000  530.00000     OPLS hydrocarbons ff (jtr 5-14-91)
C=  C=     1.46000  385.00000     wlj 1,3-diene 3/97
C=  CM     1.34000  549.00000     wlj
C=  CT     1.51000  317.00000     wlj
C=  CW     1.36500  549.00000
C=  HC     1.08000  340.00000     wlj
C=  N=     1.42800  415.00000     wlj azadiene 9/02
CA  CA     1.40000  469.00000     TRP,TYR,PHE
CA  CB     1.40400  469.00000     ADE
CA  CC     1.40000  469.00000     TRP
CA  CD     1.40000  469.00000     PHE,TYR
CA  CJ     1.43300  427.00000     CYT
CA  CM     1.43300  427.00000
CA  CN     1.40000  469.00000     TRP
CA  CT     1.51000  317.00000     PHE,TYR
CA  CU     1.42100  469.00000     "
CA  CW     1.36700  546.00000     pyrrole - wlj
CA  CY     1.49000  317.00000     wlj
CA  CZ     1.45100  400.00000     wlj 9/98
CA  Cl     1.72500  300.00000     wlj
CA  DM     0.30000  367.00000     wlj
CA  F      1.35400  420.00000     wlj
CA  HA     1.08000  367.00000     PHE, etc.
CA  I      2.08000  250.00000     wlj
CA  N      1.38100  427.00000     Added DSM (from GUA)
CA  N2     1.34000  481.00000     ARG
CA  N3     1.45000  400.00000     LYS(OL)
CA  NA     1.38100  427.00000     GUA
CA  NB     1.39100  414.00000     Added DSM (from CB-NB)
CA  NC     1.33900  483.00000     ADE,GUA,CYT
CA  NO     1.46000  400.00000     wlj nitro
CA  NT     1.34000  481.00000     wj/rr anilines
CA  NY     1.38500  382.00000     jtr - neutral Arg; MLL
CA  NZ     1.41000  400.00000     wlj 10/04  isonitrile
CA  OH     1.36400  450.00000
CA  OS     1.36400  450.00000     wlj
CA  P      1.78000  220.00000
CA  S      1.76000  250.00000     thioanisole             copy from CW-S          rcr HIVRT
CA  SH     1.74000  250.00000     wlj
CA  SY     1.77000  340.00000
CB  CB     1.37000  520.00000     ADE,GUA
CB  CC     1.37000  520.00000     Added DSM (from CB-CB)
CB  CD     1.40000  469.00000     TRP
CB  CN     1.41900  447.00000     TRP
CB  CS     1.42400  469.00000     "
CB  CT     1.51000  317.00000     Added DSM (from CA-CT)
CB  N*     1.37400  436.00000     ADE,GUA
CB  NA     1.37400  436.00000     wlj
CB  NB     1.39100  414.00000     ADE,GUA,HIS
CB  NC     1.35400  461.00000     ADE,GUA
CB  OS     1.36000  340.00000     wlj
CC  CD     1.40000  469.00000     TRP
CC  CF     1.37500  512.00000     HIS
CC  CG     1.37100  518.00000     HIS
CC  CT     1.50400  317.00000     HIS
CC  CV     1.37500  512.00000     HIS
CC  CW     1.37100  518.00000     HIS
CC  NA     1.38500  422.00000     HIS
CC  NB     1.39400  410.00000     ADE,GUA,HIS
CD  CD     1.40000  469.00000     TRP,TYR,PHE
CD  CN     1.40000  469.00000     TRP
CE  N*     1.37100  440.00000     ADE,GUA
CE  NB     1.30400  529.00000     ADE,GUA
CF  NB     1.39400  410.00000     ADE,GUA,HIS
CG  NA     1.38100  427.00000     TRP,HIS
CH  CH     1.52600  260.00000     SUG(as in CH-C2),ILE
CH  N      1.44900  337.00000     AA
CH  N*     1.47500  337.00000     ADE,GUA,CYT,URA
CH  NT     1.44800  382.00000     wlj - MM3 based
CH  OH     1.42500  386.00000     RSUG,THR
CH  OS     1.42500  320.00000     SUG
CI  NC     1.32400  502.00000     ADE
CJ  CJ     1.35000  549.00000     URA,CYT
CJ  CM     1.35000  549.00000     THY
CJ  N*     1.36500  448.00000     URA,CYT
CK  H5     1.08000  367.00000
CK  HA     1.08000  340.00000
CK  N*     1.37100  440.00000
CK  NA     1.37100  440.00000
CK  NB     1.30400  529.00000
CM  CM     1.34000  549.00000     wlj
CM  CT     1.51000  317.00000     wlj
CM  CY     1.51000  317.00000     hept,                   copy from CM-CT         rcr HIVRT
CM  Cl     1.72500  300.00000     wlj
CM  F      1.34000  420.00000     wlj
CM  H4     1.08000  367.00000
CM  HC     1.08000  340.00000     wlj
CM  N*     1.36500  448.00000
CM  NA     1.36500  448.00000     copy from above for CytH+ (jtr 5-14-91)
CM  OH     1.37000  450.00000     wlj
CM  OS     1.37000  450.00000     wlj
CM  S      1.76000  250.00000     hept,                   copy from CW-S          rcr HIVRT
CN  NA     1.38000  428.00000     TRP
CO  CT     1.52900  268.00000     =CT-CT - wd 3/95
CO  HC     1.09000  340.00000     =CT-HC - wd 3/95
CO  N*     1.47500  337.00000     jtr (12/7/01)
CO  OH     1.38000  320.00000     =CO-OS - wd 3/96
CO  OS     1.38000  320.00000     Acetal - wlj 2/93
CP  NA     1.34300  477.00000     HIS
CP  NB     1.33500  488.00000     HIS(MOD)
CQ  H5     1.08000  367.00000
CQ  HA     1.08000  367.00000
CQ  N      1.38100  427.00000     wlj
CQ  N2     1.34000  481.00000     wlj
CQ  NC     1.32400  502.00000
CR  CS     1.37000  520.00000     wj
CR  H5     1.08000  367.00000
CR  HA     1.08000  367.00000
CR  N2     1.34000  481.00000     wlj
CR  NA     1.34300  477.00000     HIS
CR  NB     1.33500  488.00000     HIS(MOD)
CR  NC     1.35400  461.00000     wj
CR  OS     1.35700  462.00000     "
CR  S      1.76000  250.00000     wlj
CS  CS     1.42400  469.00000     "
CS  CT     1.49500  317.00000     wlj
CS  CW     1.36700  546.00000     wj/nm
CS  HA     1.08000  367.00000     "
CT  CT     1.52900  268.00000     CHARMM 22 parameter file
CT  CV     1.50400  317.00000     jtr: HIE CB-CG
CT  CW     1.50400  317.00000     jtr: HID CB-CG
CT  CX     1.50400  317.00000     jtr: HIP CB-CG
CT  CY     1.51000  280.00000     "
CT  CZ     1.47000  390.00000     wlj 9/98 do 11/98
CT  Cl     1.78100  245.00000     wlj - from MM2 (Tet 31, 1971 (75))
CT  DM     0.30000  340.00000     wlj
CT  F      1.33200  367.00000     PAK CT-F for CHF3 (emd 5-09-94)
CT  HC     1.09000  340.00000     CHARMM 22 parameter file
CT  I      2.19000  200.00000     wlj see JPOC 7, 420 (1994)
CT  N      1.44900  337.00000
CT  N$     1.44900  337.00000     wj
CT  N*     1.47500  337.00000
CT  N2     1.46300  337.00000     ARG(OL)
CT  N3     1.47100  367.00000     LYS(OL)
CT  NA     1.47500  337.00000     copy from above for CytH+ (jtr 5-14-91)
CT  NC     1.44900  337.00000     wj azide
CT  NM     1.44900  337.00000
CT  NO     1.49000  375.00000     wlj nitro
CT  NT     1.44800  382.00000     "
CT  NY     1.44800  382.00000     jtr - neutral Arg; MLL
CT  NZ     1.43000  390.00000     wlj 10/04  isonitrile
CT  OH     1.41000  320.00000
CT  OS     1.41000  320.00000
CT  P      1.84300  212.00000     wlj 11/95 MM3 based JACS 114, 8536 (92)
CT  P+     1.82000  212.00000     wlj 9/97
CT  S      1.81000  222.00000     CYX(OL)
CT  SH     1.81000  222.00000     CYS(OL)
CT  SY     1.77000  340.00000
CT  SZ     1.79000  340.00000
CT  Si     1.86000  187.00000     wlj MMFF-based
CU  CW     1.37000  520.00000     wlj
CU  HA     1.08000  367.00000     "
CU  NB     1.32000  410.00000     "
CV  CW     1.37000  520.00000     wlj imidazole
CV  H4     1.08000  367.00000
CV  HA     1.08000  367.00000
CV  NB     1.39400  410.00000     ADE,GUA,HIS
CW  CW     1.37500  512.00000
CW  H4     1.08000  367.00000
CW  HA     1.08000  367.00000     pyrrole - wlj
CW  NA     1.38100  427.00000     TRP,HIS
CW  NB     1.39400  410.00000
CW  OS     1.36000  340.00000     Furan  - wlj 4/97
CW  S      1.74000  250.00000     wlj
CX  CX     1.37000  520.00000     copy from CV-CW for HIP
CX  HA     1.08000  367.00000     jtr - HIP
CX  NA     1.38100  427.00000     jtr - HIP
CY  CY     1.52000  260.00000     cyclopropanes, cyclobutanes - wlj
CY  CZ     1.45100  400.00000     wlj
CY  HC     1.08800  340.00000     "
CY  N      1.44900  337.00000     wj
CY  N$     1.44900  337.00000     wj
CY  NT     1.44800  382.00000     nev,                    copy from CT-NT         rcr HIVRT
CY  S      1.81000  222.00000     wj
CZ  CZ     1.21000 1150.00000     do 11/98 - JPOC, 9, 191 (1996)
CZ  Cl     1.63700  330.00000     wlj
CZ  F      1.27900  450.00000     wlj
CZ  HC     1.08000  420.00000     do 01/99 - JPOC, 9, 191 (1996)
CZ  NZ     1.15700  650.00000     wlj 9/98
Cl  DM     0.30000  300.00000     wlj
Cl  OS     1.69000  200.00000     wlj
Cl  Si     2.02000  223.00000     wlj
DM  F      0.30000  300.00000     wlj
DM  HA     0.30000  340.00000     wlj
DM  HC     0.30000  340.00000     wlj
DM  HO     0.10000  340.00000     wlj
DM  HS     0.10000  340.00000     wlj
DM  NB     0.30000  367.00000     wlj
DM  NC     0.30000  367.00000     wlj
DM  OH     0.30000  340.00000     wlj
DM  OS     0.30000  340.00000     wlj
DM  OY     0.30000  340.00000     wlj
DM  S      0.50000  340.00000     wlj
DM  SZ     0.50000  340.00000     wlj
F   Si     1.57000  461.00000     wlj
H   N      1.01000  434.00000     AA
H   N*     1.01000  434.00000
H   N2     1.01000  434.00000     URA,GUA,HIS
H   N3     1.01000  434.00000
H   NA     1.01000  434.00000     URA,GUA,HIS
H   NT     1.01000  434.00000
H   NY     1.01000  434.00000     jtr - neutral Arg; MLL
H   NZ     1.01000  434.00000     jtr - neutral Arg; MLL
H   Si     1.48000  166.00000     wlj
H2  N      1.01000  434.00000     AA
H2  N2     1.01000  434.00000     ADE,GUA,CYT,GLN,ASN,ARG
H3  N2     1.01000  434.00000     ADE,GUA,CYT,GLN,ASN,ARG
H3  N3     1.01000  434.00000     LYS(OL)
HC  Si     1.48000  166.00000     wlj stretching
HO  OH     0.94500  553.00000     SUG(OL) wlj mod 0.96 -> 0.945
HO  OS     0.94500  553.00000     SUG(OL)      6/6/94
HS  SH     1.33600  274.00000     CYS(OL)
HW  HW     1.51390   38.25000     "        "      "        for TIP3F (HW-HW)
HW  OW     0.95720  529.60000     J Phys Chem 91, 3349 (1987) for TIP3F (OW-HW)
I   Si     2.44000  108.00000     wlj
N   OH     1.38000  400.00000     wlj
N   SY     1.67000  434.00000
N   Zn     2.05000   40.00000     Merz, JACS 113, 8262 (1991)
NA  NB     1.34900  400.00000     "
NB  NB     1.28000  400.00000     " could be N-N or N=N
NB  OS     1.39900  462.00000     "
NC  NC     1.32000  500.00000     wlj pyridazine
NC  NZ     1.24000  550.00000     wlj  azide
NO  ON     1.22500  550.00000     wlj nitro
NT  NT     1.44500  350.00000     wlj
NT  OH     1.45000  320.00000     wlj
NT  OS     1.45000  320.00000     wlj
NT  SY     1.77000  340.00000     nev,                    copy from SY-CT         rcr HIVRT
NT  Si     1.74000  266.00000     wlj
NZ  NZ     1.12000  550.00000     wlj  azide
O   P      1.48000  525.00000
O2  P      1.48000  525.00000     SUG(OL)
OH  OS     1.47000  250.00000     wlj
OH  P      1.61000  230.00000     SUG(OL)
OH  Si     1.64000  374.00000     wlj
OH  Zn     1.80000   94.00000     "
OS  OS     1.47000  250.00000     wlj
OS  P      1.61000  230.00000     SUG(OL)
OS  Si     1.64000  374.00000     wlj
OU  U      1.80000  500.00000     J Phys Chem 97, 5685 (1993)
OW  Zn     2.05000   40.00000     "
OY  SY     1.44000  700.00000
OY  SZ     1.53000  700.00000
P   Si     2.25000  108.00000     wlj
S   S      2.03800  166.00000     CYX(OL)  SCHERAGA
S   Si     2.15000  144.00000     wlj
Si  Si     2.32000   94.00000     wlj for all Si
