annotate tools/rdock/data/masses.rtf @ 0:bc03dbb6eb37 draft

planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty

* ...
* ...
* Copyright (c) 1986, 1987, 1988, 1989, 1990, 1991, 1992
* Molecular Simulations Incorporated
* Confidential and Proprietary: All Rights Reserved
* ...
* ....
* TEMPLATE FOR CREATING CHARMm RTF file 
* ....
*     (%_m) replaced by first 4 characters of molecule name
*           in QUANTA (if used)
* ..
* Build RTF for %m
* ...
* sorted alphabetically; metals follow organics
* Atom type numbers 201-229 are reserved for special QUANTA display atom types.
* Last current active number is 234.
*
   22    0
MASS     7 B     10.81    B  ! Boron
MASS    14 C     12.01100 C  ! Carbonyl or Guanidinium carbon (RBT::SP2)
MASS   190 C3    12.01100 C  ! Carbonyl carbon in 3-membered aliphatic ring (RBT::SP2)
MASS   192 C4    12.01100 C  ! Carbonyl carbons in 4-membered aliphatic ring (RBT::SP2)
MASS    21 C5R   12.01100 C  ! Aromatic carbon in a five membered ring (RBT::SP2)
MASS    23 C5RE  13.01900 C  ! Extended aromatic carbon in five membered ring (RBT::SP2)
MASS    28 C5RP  12.01100 C  ! for Aryl-Aryl bond between C5R rings (RBT::SP2)
MASS   189 C5RQ  12.01100 C  ! for second Ar-Ar bond between C5RP rings (ortho) (RBT::SP2)
MASS    22 C6R   12.01100 C  ! Aromatic carbon in a six  membered ring (RBT::SP2)
MASS    24 C6RE  13.01900 C  ! Extended aromatic carbon in six membered ring (RBT::SP2)
MASS    29 C6RP  12.01100 C  ! for Aryl-Aryl bond between C6R rings (RBT::SP2)
MASS   194 C6RQ  12.01100 C  ! Carbon of C6RP type ortho to C6RP pair (RBT::SP2)
MASS   230 CF1   12.01100 C  ! Carbon with one Fluorine (RBT::SP3)
MASS   231 CF2   12.01100 C  ! Carbon with two Fluorines (RBT::SP3)
MASS   232 CF3   12.01100 C  ! Carbons with three Fluorines (RBT::SP3)
MASS    11 CH1E  13.01900 C  ! Extended atom carbon with one hydrogen (RBT::SP3)
MASS    12 CH2E  14.02700 C  ! Extended atom carbon with two hydrogens (RBT::SP3)
MASS    13 CH3E  15.03500 C  ! Extended atom carbon with three hydrogens (RBT::SP3)
MASS    15 CM    12.01100 C  ! Carbonmonoxide, or other triply bonded, carbon (RBT::SP)
MASS   199 CP3   12.01100 C  ! Carbon on nitrogen in proline ring (RBT::SP3)
MASS   197 CPH1  12.01100 C  ! CG and CD2 carbons in histidine ring (RBT::SP2)
MASS   198 CPH2  12.01100 C  ! CE1 carbon in histidine ring (RBT::SP2)
MASS   195 CQ66  12.01100 C  ! Third adjacent pair of CR66 types in fused rings (RBT::SP2)
MASS    25 CR55  12.01100 C  ! Aromatic carbon-merged five membered rings (RBT::SP2)
MASS    26 CR56  12.01100 C  ! Aromatic carbon-merged five/six membered rings (RBT::SP2)
MASS    27 CR66  12.01100 C  ! Aromatic carbon-merged six membered rings (RBT::SP2)
MASS   196 CS66  12.01100 C  ! Second adjacent pair of CR66 types in fused rings (RBT::SP2)
MASS    10 CT    12.01100 C  ! Aliphatic carbon (tetrahedral) (RBT::SP3)
MASS   191 CT3   12.01100 C  ! in 3-membered aliphatic ring, usually tetrahedral (RBT::SP3)
MASS   193 CT4   12.01100 C  ! in 4-membered aliphatic ring, usually tetrahedral (RBT::SP3)
MASS    16 CUA1  12.01100 C  ! Carbon in double bond, first pair (RBT::SP2)
MASS    17 CUA2  12.01100 C  ! Carbon in double bond, second conjugated pair (RBT::SP2)  
MASS    20 CUA3  12.01100 C  ! Carbon in double bond, third conjugated pair (RBT::SP2)
MASS    18 CUY1  12.01100 C  ! Carbon in triple bond, first pair (RBT::SP)
MASS    19 CUY2  12.01100 C  ! Carbon in triple bond, second conjugated pair (RBT::SP)
MASS     1 H      1.00800 H  ! Hydrogen bonding hydrogen (neutral group) (RBT::SP3)
MASS     3 HA     1.00800 H  ! Aliphatic or aromatic hydrogen (RBT::SP3)
MASS     2 HC     1.00800 H  ! Hydrogen bonding hydrogen (charged group) (RBT::SP3)
MASS     9 HMU    1.00800 H  ! Mu-bonded hydrogen for metals and boron-hydride (RBT::SP3)
MASS     8 HO     1.00800 H  ! Hydrogen on an alcohol oxygen (RBT::SP3)
MASS     4 HT     1.00800 H  ! TIPS3P water model hydrogen (RBT::SP3)
MASS    31 N     14.00670 N  ! Nitrogen; planar-valence of 3, i.e. nitrile, etc. (RBT::TRI)
MASS   234 N3    14.00670 N  ! Nitrogen in a three membered ring (RBT::SP3)
MASS    34 N5R   14.00670 N  ! Nitrogen in a five membered aromatic ring (RBT::TRI)
MASS    30 N5RP  14.00670 N  ! for Ar-Ar bond between five membered rings (RBT::TRI)
MASS    35 N6R   14.00670 N  ! Nitrogen in a six membered aromatic ring (RBT::SP2)
MASS    39 N6RP  14.00670 N  ! for Aryl-Aryl bond between six membered rings (RBT::SP2)
MASS    37 NC    14.00670 N  ! Charged guanidinium-type nitrogen (RBT::TRI)
MASS   186 NC2   14.00670 N  ! for neutral guanidinium group - Arg sidechain (RBT::SP2) 
MASS    38 NO2   14.00670 N  ! Nitrogen in nitro, or related, group (RBT::TRI)
MASS    32 NP    14.00670 N  ! Nitrogen in peptide, amide, or related, group (RBT::TRI)
MASS   183 NR1   14.00670 N  ! Protonated nitrogen in neutral histidine ring (RBT::TRI)
MASS   184 NR2   14.00670 N  ! Unprotonated nitrogen in neutral histidine ring (RBT::SP2)
MASS   185 NR3   14.00670 N  ! Nitrogens in charged histidine ring (RBT::SP2)
MASS   182 NR55  14.00670 N  ! N at fused bond between two 5-membered aromatics (RBT::SP2)
MASS   180 NR56  14.00670 N  ! N at fused bond between 5 and 6-membered aryls (RBT::SP2)
MASS   181 NR66  14.00670 N  ! N at fused bond between two 6-membered aromatics (RBT::SP2)
MASS    36 NT    14.00670 N  ! Nitrogen (tetrahedral), i.e. Amine, etc. (RBT::SP3)
MASS    33 NX    14.00670 N  ! Proline nitrogen, or similar (RBT::TRI)
MASS    40 O     15.99940 O  ! Carbonyl oxygen for amides, or related structures (RBT::SP2)
MASS    56 O2M   15.99940 O  ! Oxygen in Si-O-Al or Al-O-Al bond (RBT::SP3)
MASS    52 O5R   15.99940 O  ! Oxygen in 5 membered aromatic ring-radicals, etc. (RBT::SP3)
MASS    53 O6R   15.99940 O  ! Oxygen in 6 membered aromatic ring-radicals, etc. (RBT::SP3)
MASS    41 OA    15.99940 O  ! Carbonyl oxygen for aldehydes, or related (RBT::SP2)
MASS    51 OAC   15.99940 O  ! Carbonyl oxygen for acids, or related (RBT::SP2)
MASS    43 OC    15.99940 O  ! Charged oxygen (RBT::SP3)
MASS    50 OE    15.99940 O  ! Ether oxygen / Acetal oxygen (RBT::SP3)
MASS    47 OH2   15.99940 O  ! ST2  water model oxygen (RBT::SP3)
MASS    42 OK    15.99940 O  ! Carbonyl oxygen for ketones, or related (RBT::SP2)
MASS    48 OM    15.99940 O  ! Carbonmonoxide, or other triply bonded, oxygen
MASS    49 OS    15.99940 O  ! Ester oxygen (RBT::TRI)
MASS    57 OSH    0.00000 O  ! Massless O for zeolites, or related cage cmpds.
MASS    55 OSI   15.99940 O  ! Oxygen in Si-O-Si bond (RBT::SP3)
MASS    45 OT    15.99940 O  ! Hydroxyl oxygen (tetrahedral) or Ionizable acid (RBT::SP3)
MASS    46 OW    15.99940 O  ! TIP3P water model oxygen (RBT::SP3)
MASS    64 P6R   30.9738  P  ! Phosphorous in aromatic 6-membered ring (RBT::SP3)
MASS    61 PO3   30.9738  P  ! Phosphorous bonded to three oxygens (RBT::SP2)
MASS    62 PO4   30.9738  P  ! Phosphorous bonded to four oxygens (RBT::SP2)
MASS    60 PT    30.9738  P  ! Phosphorous, general; usually tetrahedral (RBT::SP3)
MASS    63 PUA1  30.9738  P  ! Phosphorous double bond 
MASS   233 PUY1  30.9738  P  ! Triple bonded phosphorus
MASS    72 S5R   32.0600  S  ! Sulphur in a five membered aromatic ring (RBT::SP3)
MASS    73 S6R   32.0600  S  ! Sulphur in a six membered aromatic ring (RBT::SP3)
MASS    74 SE    32.060   S  ! Thioether sulphur (RBT::SP3)
MASS    71 SH1E  33.06800 S  ! Extended atom sulphur with one hydrogen (RBT::SP3)
MASS    75 SK    32.060   S  ! Thioketone sulphur (RBT::SP2)
MASS    76 SO1   32.0600  S  ! Sulphur bonded to one oxygen (RBT::SP3)
MASS    77 SO2   32.0600  S  ! Sulphur bonded to two oxygens (RBT::SP3)
MASS    78 SO3   32.0600  S  ! Sulphur bonded to three oxygens (RBT::SP2)
MASS    79 SO4   32.0600  S  ! Sulphur bonded to four oxygens (RBT::SP2)
MASS    70 ST    32.06000 S  ! Sulphur, general; usually tetrahedral (RBT::SP3)
MASS    94 XBR   79.904   Br ! Bromine
MASS    93 XCL   35.45300 Cl ! Chlorine
MASS    92 XF    18.99840 F  ! Fluorine
MASS    95 XI   126.9045  I  ! Iodine
MASS    91 MAL   26.9815  Al ! ALuminum
MASS     6 MBE    9.01218 Be ! Beryllium
MASS    84 MCA   40.080   Ca ! Calcium 
MASS    83 MK    39.098   K  ! Potassium
MASS    80 MLI    6.941   Li ! Lithium
MASS    82 MMG   24.305   Mg ! Magnesium
MASS    81 MNA   22.9898  Na ! Sodium
MASS    90 MSI   28.0855  Si ! Silicon
MASS   177 MSIU 28.08550  Si ! Silicon when as double bond
MASS	86 MFE   55.85    Fe ! Iron 
MASS    87 MZN  65.3800   Zn ! Zinc (Added DM 30/7/2001)

* 4 Jan 1999 (DM) Added old types from
* /darius/dsk1/progs/insightII/insight97/data/xplor/toppar/topallhdg.pro
* just to keep rbscore happy. The numeric force field types are ficticious
* and will not be recognised by Charmm
MASS   301 CX    12.011   C  ! (RBT::SP2)
MASS   302 CW    12.011   C  ! (RBT::SP2)
MASS   303 CN    12.011   C  ! (RBT::SP2)
MASS   304 CA    12.011   C  ! (RBT::SP2)
MASS   305 CB    12.011   C  ! (RBT::SP2)
MASS   306 CC    12.011   C  ! (RBT::SP2)
MASS   307 CV    12.011   C  ! (RBT::SP2)
MASS   308 CR    12.011   C  ! (RBT::SP2)
MASS   309 CP    12.011   C  ! Proline carbon CG,CD (RBT::SP3)
MASS   310 NA    14.007   N  ! (RBT::TRI)
MASS   311 NB    14.007   N  ! (RBT::TRI)
MASS   312 NH1   14.007   N  ! (RBT::TRI)
MASS   313 NH2   14.007   N  ! (RBT::TRI)
MASS   314 NH3   14.007   N  ! (RBT::SP3)
MASS   315 OH    15.999   O  ! (RBT::SP3)
MASS   316 S     32.060   S  ! (RBT::SP3)

* 4 Jan 1999 (DM) Added old types from
* /darius/dsk1/progs/insightII/insight97/data/xplor/toppar/topallhdg.dna
* just to keep rbscore happy. The numeric force field types are ficticious
* and will not be recognised by Charmm
MASS   400 H2     1.00800 H  ! (RBT::SP3)
MASS   401 CH    12.01100 C  ! (RBT::SP3)
MASS   402 C2    12.01100 C  ! (RBT::SP3)
MASS   403 CE    12.01100 C  ! (RBT::SP2)
MASS   404 CF    12.01100 C  ! (RBT::SP2)
MASS   405 CS    12.01100 C  ! (RBT::SP2)
MASS   406 N2    14.00670 N  ! (RBT::TRI) Corrected DM 23/8/1999
MASS   407 NS    14.00670 N  ! (RBT::TRI)
MASS   408 NH2E  16.02270 N  ! (RBT::SP3)
MASS   409 O2    15.99940 O  ! (RBT::SP3)
MASS   411 SD    22.98980 Na !
MASS   412 P     30.97400 P  ! (RBT::SP3)
MASS   413 BR    79.90400 Br !
MASS   414 MG    24.30500 Mg !

* 8 Jun 1999 (DM) Added types to keep wtTARrbt158.psf happy
MASS   450 HE     1.00800 H  ! (RBT::SP3)

* 18 Jan 2001 (DM) Dummy atom type
MASS   666 DUM    0.00000 DU ! Dummy atom

* Charmm 27 additions 
MASS     5 H      1.00800 H  ! Nonpolar H prom charmm27 all-atom FF (RBT::SP3)
MASS    54 HG     1.00800 H  ! Nonpolar H prom charmm27 all-atom FF (RBT::SP3)
MASS    58 NE    14.00670 N  ! charmm27 N

RESI  XXXX  0.0    

END