------------------------------------------------------- Amber 9 PBSA Scripps/UCSF 2006 ------------------------------------------------------- | Run on 10/30/2008 at 14:40:26 [-O]verwriting output File Assignments: | MDIN: pbsa.in | MDOUT: pbsa_lig.5.out |INPCRD: ./snapshot_lig.crd.5 | PARM: ../../pdz1/ligand/DSLA.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: File generated by mm_pbsa.pl. Using PB &cntrl ntf = 1, ntb = 0, igb = 10, dielc = 1.0, cut = 999.0, nsnb = 99999, scnb = 2.0, scee = 1.2, imin = 1, maxcyc = 0, ntmin = 2, &end &pb epsin = 1.0, epsout = 80.0, istrng = 0, radiopt = 0, sprob = 1.4, space = 0.5, maxitn = 1000, npopt = 1, cavity_surften = 0.0072, cavity_offset = 0.00, npbverb= 1 &end -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 06/26/03 Time = 02:39:55 NATOM = 55 NTYPES = 10 NBONH = 27 MBONA = 27 NTHETH = 61 MTHETA = 36 NPHIH = 103 MPHIA = 56 NHPARM = 0 NPARM = 0 NNB = 291 NRES = 4 NBONA = 27 NTHETA = 36 NPHIA = 56 NUMBND = 11 NUMANG = 16 NPTRA = 18 NATYP = 10 NPHB = 0 IFBOX = 0 NMXRS = 19 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 2073 | Hollerith 336 | Integer 22588 | Max Pairs 1 | Max Rstack 1 | Max Istack 1 | Total 105 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- Amber topology and parameter file for the molecule set DSLA General flags: imin = 1, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 10, nsnb = 99999 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 0, ncyc = 10, ntmin = 2 dx0 = 0.01000, drms = 0.00010 ======== Implicit Solvent Initialization ======== Max Nonbonded Pairs: 1513 1513 1513 no. of atoms processed in PB initialization: 55 NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI 1 ASP N N3 0.078200 0.738200 0.881500 1.400000 1.400000 2 ASP CA CT 0.029200 0.143300 1.386300 1.548000 1.548000 3 ASP C C 0.562100 0.562100 -0.027300 1.548000 1.548000 4 ASP O O -0.588900 -0.588900 -0.026800 1.348000 1.348000 5 ASP CB CT -0.023500 -0.057300 0.905400 1.548000 1.548000 6 ASP CG C 0.819400 0.819400 -0.854700 1.548000 1.548000 7 ASP OD1 O2 -0.808400 -0.808400 0.011000 1.348000 1.348000 8 ASP OD2 O2 -0.808400 -0.808400 0.011000 1.348000 1.348000 9 ASP H1 H 0.220000 0.000000 0.000000 1.100000 1.100000 10 ASP H2 H 0.220000 0.000000 0.000000 1.100000 1.100000 11 ASP H3 H 0.220000 0.000000 0.000000 1.100000 1.100000 12 ASP HA HP 0.114100 0.000000 0.000000 1.100000 1.100000 13 ASP HB2 HC -0.016900 0.000000 0.000000 1.100000 1.100000 14 ASP HB3 HC -0.016900 0.000000 0.000000 1.100000 1.100000 15 SER N N -0.415700 -0.143800 0.477700 1.400000 1.400000 16 SER CA CT -0.024900 0.059400 0.795000 1.548000 1.548000 17 SER C C 0.597300 0.597300 -0.055000 1.548000 1.548000 18 SER O O -0.567900 -0.567900 0.029400 1.348000 1.348000 19 SER CB CT 0.211700 0.282100 0.114400 1.548000 1.548000 20 SER OG OH -0.654600 -0.227100 0.055000 1.348000 1.348000 21 SER H H 0.271900 0.000000 0.000000 1.100000 1.100000 22 SER HA H1 0.084300 0.000000 0.000000 1.100000 1.100000 23 SER HB2 H1 0.035200 0.000000 0.000000 1.100000 1.100000 24 SER HB3 H1 0.035200 0.000000 0.000000 1.100000 1.100000 25 SER HG HO 0.427500 0.000000 0.000000 1.100000 1.100000 26 LEU N N -0.415700 -0.143800 0.493900 1.400000 1.400000 27 LEU CA CT -0.051800 0.040400 0.475100 1.548000 1.548000 28 LEU C C 0.597300 0.597300 -0.044200 1.548000 1.548000 29 LEU O O -0.567900 -0.567900 0.029400 1.348000 1.348000 30 LEU CB CT -0.110200 -0.018800 0.338600 1.548000 1.548000 31 LEU CG CT 0.353100 0.317000 0.074000 1.548000 1.548000 32 LEU CD1 CT -0.412100 -0.112100 0.204900 1.548000 1.548000 33 LEU CD2 CT -0.412100 -0.112100 0.204900 1.548000 1.548000 34 LEU H H 0.271900 0.000000 0.000000 1.100000 1.100000 35 LEU HA H1 0.092200 0.000000 0.000000 1.100000 1.100000 36 LEU HB2 HC 0.045700 0.000000 0.000000 1.100000 1.100000 37 LEU HB3 HC 0.045700 0.000000 0.000000 1.100000 1.100000 38 LEU HG HC -0.036100 0.000000 0.000000 1.100000 1.100000 39 LEU HD11 HC 0.100000 0.000000 0.000000 1.100000 1.100000 40 LEU HD12 HC 0.100000 0.000000 0.000000 1.100000 1.100000 41 LEU HD13 HC 0.100000 0.000000 0.000000 1.100000 1.100000 42 LEU HD21 HC 0.100000 0.000000 0.000000 1.100000 1.100000 43 LEU HD22 HC 0.100000 0.000000 0.000000 1.100000 1.100000 44 LEU HD23 HC 0.100000 0.000000 0.000000 1.100000 1.100000 45 ALA N N -0.382100 -0.114000 0.443200 1.400000 1.400000 46 ALA CA CT -0.174700 -0.040100 0.680900 1.548000 1.548000 47 ALA C C 0.773100 0.773100 -0.878000 1.548000 1.548000 48 ALA O O2 -0.805500 -0.805500 -0.032400 1.348000 1.348000 49 ALA CB CT -0.209300 0.061900 0.021800 1.548000 1.548000 50 ALA OXT O2 -0.805500 -0.805500 -0.032400 1.348000 1.348000 51 ALA H H 0.268100 0.000000 0.000000 1.100000 1.100000 52 ALA HA H1 0.134600 0.000000 0.000000 1.100000 1.100000 53 ALA HB2 HC 0.097400 0.000000 0.000000 1.100000 1.100000 54 ALA HB3 HC 0.097400 0.000000 0.000000 1.100000 1.100000 55 ALA HB1 HC 0.076400 0.000000 0.000000 1.100000 1.100000 total system charges (+/-) for PB -0.9301 7.3790 -8.3091 cavity_surften = 0.0072 cavity_offset = 0.0000 SAS Surface: surface dots generated: 366 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- Amber topology and parameter file for the molecule set complex_dsla_nowat begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NB-update: residue-based nb list 1199 NB-update: atom-based nb list 1162 ======== Setting up Grid Parameters ======== Using bounding box for grid setup Bounding Box Center: 9.000 3.000 -4.500 Xmin, Xmax, Xmax-Xmin: 2.597 15.482 12.885 Ymin, Ymax, Ymax-Ymin: -1.509 7.303 8.812 Zmin, Zmax, Zmax-Zmin: -12.509 3.125 15.634 beginning box center at level 1 9.000 3.000 -4.500 beginning box center at level 2 9.000 3.000 -4.500 Grid dimension at level 1 7 5 9 Grid origin corrected at level 1 -7.000 -9.000 -24.500 Grid dimension at level 2 41 33 45 Grid origin corrected at level 2 -1.500 -5.500 -16.000 PB Bomb in setgrd(): focusing grid too large 2 reset fillratio to a larger number 2.000