AMBER FF molecular topology data for Phospho-tyrosine residue in the -2 charge state. The PDB format data is just for reference, and contains the new charges in the last column. The prep input and parm98.dat additions are both needed to utilize this residue in AMBER. Please send questions to youngm@rockefeller.edu. PDB format: ============================================================================= ATOM 7067 N PT2 527 -4.518 16.252 19.116 1.60 -0.43 ATOM 7068 CA PT2 527 -4.128 17.361 18.260 1.64 0.00 ATOM 7069 C PT2 527 -3.626 18.398 19.251 1.64 0.62 ATOM 7070 O PT2 527 -4.249 18.595 20.288 1.53 -0.59 ATOM 7071 CB PT2 527 -5.337 17.952 17.531 1.64 0.00 ATOM 7072 CG PT2 527 -5.845 17.072 16.413 1.64 -0.01 ATOM 7073 CD1 PT2 527 -5.502 17.342 15.103 1.64 -0.29 ATOM 7074 CD2 PT2 527 -6.692 16.031 16.706 1.64 -0.29 ATOM 7075 CE1 PT2 527 -6.020 16.560 14.074 1.64 -0.39 ATOM 7076 CE2 PT2 527 -7.215 15.244 15.689 1.64 -0.39 ATOM 7077 CZ PT2 527 -6.897 15.491 14.348 1.64 0.85 ATOM 7078 OH PT2 527 -7.548 14.647 13.200 1.54 -0.80 ATOM 7079 H PT2 527 -5.112 16.403 19.747 1.05 0.28 ATOM 7080 HB2 PT2 527 -5.223 18.899 17.231 1.45 0.03 ATOM 7081 HD2 PT2 527 -6.930 15.823 17.654 1.44 0.16 ATOM 7082 P PT2 527 -7.524 13.003 12.521 1.72 1.75 ATOM 7083 O1P PT2 527 -6.380 12.159 13.022 1.53 -1.04 ATOM 7084 O2P PT2 527 -7.462 13.084 11.021 1.53 -1.04 ATOM 7085 O3P PT2 527 -8.801 12.313 12.875 1.53 -1.04 ATOM 7086 H21 PT2 527 -7.881 14.544 15.944 1.44 0.16 ATOM 7087 H22 PT2 527 -5.809 16.801 13.127 1.44 0.16 ATOM 7088 H23 PT2 527 -4.881 18.097 14.896 1.44 0.16 ATOM 7089 H24 PT2 527 -6.043 17.930 18.239 1.45 0.03 ATOM 7090 HA PT2 527 -3.377 17.120 17.645 1.41 0.09 ============================================================================= Amber prep input: (charges in the last column) ============================================================================= 0 0 0 leap-generated prep residue PT2.res PT2 INT 0 CHANGE NOMIT DU BEG 0.00000 1 DUMM DU M 0.000000 0.000000 0.000000 0.0 2 DUMM DU M 1.000000 0.000000 0.000000 0.0 3 DUMM DU M 1.000000 1.000000 0.000000 0.0 4 N N M 27.992000 -2.909000 -2.354000 -0.434400 5 H H E 27.665000 -2.662000 -3.132000 0.284100 6 CA CT M 27.772000 -2.042000 -1.212000 -0.001500 7 CB CT 3 28.290000 -0.637000 -1.501000 -0.000300 8 H24 HC E 27.943850 -0.493266 -2.428426 0.030800 9 HB2 HC E 27.921247 0.083634 -0.913908 0.030800 10 CG CA B 29.812000 -0.551000 -1.605000 -0.014300 11 CD1 CA B 30.568000 -0.422000 -0.438000 -0.286100 12 H23 HA E 30.116656 -0.387697 0.453161 0.163600 13 CE1 CA B 31.951000 -0.344000 -0.524000 -0.389600 14 H22 HA E 32.495616 -0.233536 0.307053 0.160900 15 CZ C B 32.566000 -0.385000 -1.738000 0.848300 16 CE2 CA S 31.847000 -0.512000 -2.919000 -0.389600 17 H21 HA E 32.305453 -0.518443 -3.807346 0.160900 18 OH OS S 33.959000 -0.189000 -1.814000 -0.800300 19 P P 3 35.061000 -1.370000 -1.524000 1.753500 20 O1P O2 E 35.539000 -1.827000 -2.886000 -1.038900 21 O2P O2 E 34.378000 -2.445000 -0.720000 -1.038900 22 O3P O2 E 36.153000 -0.594000 -0.760000 -1.038900 23 CD2 CA S 30.458000 -0.576000 -2.823000 -0.286100 24 HD2 HA E 29.915704 -0.652381 -3.659667 0.163600 25 HA H1 E 28.268750 -2.410870 -0.426491 0.091700 26 C C M 26.291000 -1.986000 -0.863000 0.624100 27 O O E 25.410000 -1.890000 -1.745000 -0.593400 LOOP CD2 CE2 IMPROPER CD1 CD2 CG CB CG CE1 CD1 H23 CG CE2 CD2 HD2 CZ CD1 CE1 H22 CZ CD2 CE2 H21 CE1 CE2 CZ OH -M CA N H CA +M C O DONE STOP ============================================================================= parm98.dat additions New bonds, angles and torsions for the C-C-O-P torsion (these lines should be inserted into parm98.dat in the appropriate sections) ============================================================================= # bond fconst rmin C -OS 450.0 1.364 JCC,7,(1986),230; TYR (copied, may pt2) #angle fconst rmin CA-C -OS 70.0 120.00 may (pt2) C -OS-P 100.0 120.50 may (pt2) #Etors=(PK/IDIVF)*(1+cos(PN*phi-PHASE)) #torsion IDIVF PK PHASE PN CA-C -OS-P 2 4.00 180.0 2. may ene.631g*/mp2 (pt2) =============================================================================