------------------------------------------------------- PBSA VERSION 2009 UC Irvine ------------------------------------------------------- | Run on 01/01/2004 at 13:40:26 [-O]verwriting output File Assignments: | MDIN: 1VJ5_pbsa.in | MDOUT: 1VJ5_pbsa.out |INPCRD: 1VJ5_pbsa.inpcrd | PARM: 1VJ5_pbsa.prmtop | Here is the input file: PBSA visualization input &cntrl ntx=1, imin=1, maxcyc=10000, ipb=1, inp=0, / &pb npbverb=1, istrng=0, epsout=80.0, epsin=1.0, space=1.0, accept=0.001, sprob=1.4, cutnb=2, phiout=1, phiform=0 / PB Info in pb_read(): npopt has been overwritten with inp PB Info in pb_read(): cutnb has been reset to be equal to cutfd -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 01/01/04 Time = 08:20:40 NATOM = 179 NTYPES = 11 NBONH = 90 MBONA = 89 NTHETH = 203 MTHETA = 119 NPHIH = 378 MPHIA = 274 NHPARM = 0 NPARM = 0 NNB = 968 NRES = 12 NBONA = 89 NTHETA = 119 NPHIA = 274 NUMBND = 20 NUMANG = 41 NPTRA = 30 NATYP = 15 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 6664 | Hollerith 1088 | Integer 25957 | Max Pairs 1 | Max Rstack 1 | Max Istack 1 | Total 157 kbytes -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- 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 = 1, igb = 10, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 1, ncyc = 10, ntmin = 1 dx0 = 0.01000, drms = 0.00010 ======== Implicit Solvent Initialization ======== Max Nonbonded Pairs: 16021 16021 16021 no. of atoms processed in PB initialization: 179 NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI 1 PHE N N3 0.173700 0.750000 0.927400 1.450000 1.624999 2 PHE H1 H 0.192100 0.000000 0.000000 1.100000 0.534539 3 PHE H2 H 0.192100 0.000000 0.000000 1.100000 0.534539 4 PHE H3 H 0.192100 0.000000 0.000000 1.100000 0.534539 5 PHE CA CT 0.073300 0.177400 1.593500 1.600000 1.699835 6 PHE HA HP 0.104100 0.000000 0.000000 1.100000 0.979989 7 PHE CB CT 0.033000 0.053800 0.234300 1.600000 1.699835 8 PHE HB2 HC 0.010400 0.000000 0.000000 1.100000 1.324766 9 PHE HB3 HC 0.010400 0.000000 0.000000 1.100000 1.324766 10 PHE CG CA 0.003100 0.003100 0.053400 1.600000 1.699835 11 PHE CD1 CA -0.139200 -0.001800 -0.015600 1.600000 1.699835 12 PHE HD1 HA 0.137400 0.000000 0.000000 1.100000 1.299821 13 PHE CE1 CA -0.160200 -0.016900 -0.006600 1.600000 1.699835 14 PHE HE1 HA 0.143300 0.000000 0.000000 1.100000 1.299821 15 PHE CZ CA -0.120800 0.012100 -0.021800 1.600000 1.699835 16 PHE HZ HA 0.132900 0.000000 0.000000 1.100000 1.299821 17 PHE CE2 CA -0.160300 -0.017000 -0.006600 1.600000 1.699835 18 PHE HE2 HA 0.143300 0.000000 0.000000 1.100000 1.299821 19 PHE CD2 CA -0.139100 -0.001700 -0.015600 1.600000 1.699835 20 PHE HD2 HA 0.137400 0.000000 0.000000 1.100000 1.299821 21 PHE C C 0.612300 0.612300 0.074600 1.600000 1.699835 22 PHE O O -0.571300 -0.571300 0.041000 1.420000 1.479961 23 GLY N N -0.415700 -0.143800 0.582900 1.450000 1.624999 24 GLY H H 0.271900 0.000000 0.000000 1.100000 0.534539 25 GLY CA CT -0.025200 0.114400 0.567900 1.600000 1.699835 26 GLY HA2 H1 0.069800 0.000000 0.000000 1.100000 1.235677 27 GLY HA3 H1 0.069800 0.000000 0.000000 1.100000 1.235677 28 GLY C C 0.597300 0.597300 0.000000 1.600000 1.699835 29 GLY O O -0.567900 -0.567900 0.029400 1.420000 1.479961 30 VAL N N -0.415700 -0.143800 0.462900 1.450000 1.624999 31 VAL H H 0.271900 0.000000 0.000000 1.100000 0.534539 32 VAL CA CT -0.087500 0.009400 0.731700 1.600000 1.699835 33 VAL HA H1 0.096900 0.000000 0.000000 1.100000 1.235677 34 VAL CB CT 0.298500 0.268800 0.114400 1.600000 1.699835 35 VAL HB HC -0.029700 0.000000 0.000000 1.100000 1.324766 36 VAL CG1 CT -0.319200 -0.081900 0.186900 1.600000 1.699835 37 VAL HG11 HC 0.079100 0.000000 0.000000 1.100000 1.324766 38 VAL HG12 HC 0.079100 0.000000 0.000000 1.100000 1.324766 39 VAL HG13 HC 0.079100 0.000000 0.000000 1.100000 1.324766 40 VAL CG2 CT -0.319200 -0.081900 0.186900 1.600000 1.699835 41 VAL HG21 HC 0.079100 0.000000 0.000000 1.100000 1.324766 42 VAL HG22 HC 0.079100 0.000000 0.000000 1.100000 1.324766 43 VAL HG23 HC 0.079100 0.000000 0.000000 1.100000 1.324766 44 VAL C C 0.597300 0.597300 -0.105000 1.600000 1.699835 45 VAL O O -0.567900 -0.567900 0.029400 1.420000 1.479961 46 LEU N N -0.415700 -0.143800 0.493900 1.450000 1.624999 47 LEU H H 0.271900 0.000000 0.000000 1.100000 0.534539 48 LEU CA CT -0.051800 0.040400 0.475100 1.600000 1.699835 49 LEU HA H1 0.092200 0.000000 0.000000 1.100000 1.235677 50 LEU CB CT -0.110200 -0.018800 0.338600 1.600000 1.699835 51 LEU HB2 HC 0.045700 0.000000 0.000000 1.100000 1.324766 52 LEU HB3 HC 0.045700 0.000000 0.000000 1.100000 1.324766 53 LEU CG CT 0.353100 0.317000 0.074000 1.600000 1.699835 54 LEU HG HC -0.036100 0.000000 0.000000 1.100000 1.324766 55 LEU CD1 CT -0.412100 -0.112100 0.204900 1.600000 1.699835 56 LEU HD11 HC 0.100000 0.000000 0.000000 1.100000 1.324766 57 LEU HD12 HC 0.100000 0.000000 0.000000 1.100000 1.324766 58 LEU HD13 HC 0.100000 0.000000 0.000000 1.100000 1.324766 59 LEU CD2 CT -0.412100 -0.112100 0.204900 1.600000 1.699835 60 LEU HD21 HC 0.100000 0.000000 0.000000 1.100000 1.324766 61 LEU HD22 HC 0.100000 0.000000 0.000000 1.100000 1.324766 62 LEU HD23 HC 0.100000 0.000000 0.000000 1.100000 1.324766 63 LEU C C 0.597300 0.597300 -0.074000 1.600000 1.699835 64 LEU O O -0.567900 -0.567900 0.029400 1.420000 1.479961 65 GLY N N -0.415700 -0.143800 0.567900 1.450000 1.624999 66 GLY H H 0.271900 0.000000 0.000000 1.100000 0.534539 67 GLY CA CT -0.025200 0.114400 0.567900 1.600000 1.699835 68 GLY HA2 H1 0.069800 0.000000 0.000000 1.100000 1.235677 69 GLY HA3 H1 0.069800 0.000000 0.000000 1.100000 1.235677 70 GLY C C 0.597300 0.597300 0.070600 1.600000 1.699835 71 GLY O O -0.567900 -0.567900 0.029400 1.420000 1.479961 72 ARG N N -0.347900 -0.073200 0.416400 1.450000 1.624999 73 ARG H H 0.274700 0.000000 0.000000 1.100000 0.534539 74 ARG CA CT -0.263700 -0.107700 0.617900 1.600000 1.699835 75 ARG HA H1 0.156000 0.000000 0.000000 1.100000 1.235677 76 ARG CB CT -0.000700 0.064700 0.053000 1.600000 1.699835 77 ARG HB2 HC 0.032700 0.000000 0.000000 1.100000 1.324766 78 ARG HB3 HC 0.032700 0.000000 0.000000 1.100000 1.324766 79 ARG CG CT 0.039000 0.096000 0.346700 1.600000 1.699835 80 ARG HG2 HC 0.028500 0.000000 0.000000 1.100000 1.324766 81 ARG HG3 HC 0.028500 0.000000 0.000000 1.100000 1.324766 82 ARG CD CT 0.048600 0.186000 0.098100 1.600000 1.699835 83 ARG HD2 H1 0.068700 0.000000 0.000000 1.100000 1.235677 84 ARG HD3 H1 0.068700 0.000000 0.000000 1.100000 1.235677 85 ARG NE N2 -0.529500 -0.183900 0.809700 1.450000 1.624999 86 ARG HE H 0.345600 0.000000 0.000000 1.100000 0.534539 87 ARG CZ CA 0.807600 0.807600 0.689500 1.600000 1.699835 88 ARG NH1 N2 -0.862700 0.032900 0.840500 1.450000 1.624999 89 ARG HH11 H 0.447800 0.000000 0.000000 1.100000 0.534539 90 ARG HH12 H 0.447800 0.000000 0.000000 1.100000 0.534539 91 ARG NH2 N2 -0.862700 0.032900 0.840500 1.450000 1.624999 92 ARG HH21 H 0.447800 0.000000 0.000000 1.100000 0.534539 93 ARG HH22 H 0.447800 0.000000 0.000000 1.100000 0.534539 94 ARG C C 0.734100 0.734100 -0.106800 1.600000 1.699835 95 ARG O O -0.589400 -0.589400 0.144700 1.420000 1.479961 96 THR N N -0.415700 -0.143800 0.652100 1.450000 1.624999 97 THR H H 0.271900 0.000000 0.000000 1.100000 0.534539 98 THR CA CT -0.038900 0.061800 0.885000 1.600000 1.699835 99 THR HA H1 0.100700 0.000000 0.000000 1.100000 1.235677 100 THR CB CT 0.365400 0.369700 0.114400 1.600000 1.699835 101 THR HB H1 0.004300 0.000000 0.000000 1.100000 1.235677 102 THR CG2 CT -0.243800 -0.051200 0.318500 1.600000 1.699835 103 THR HG21 HC 0.064200 0.000000 0.000000 1.100000 1.324766 104 THR HG22 HC 0.064200 0.000000 0.000000 1.100000 1.324766 105 THR HG23 HC 0.064200 0.000000 0.000000 1.100000 1.324766 106 THR OG1 OH -0.676100 -0.265900 0.103800 1.420000 1.533237 107 THR HG1 HO 0.410200 0.000000 0.000000 1.100000 0.000000 108 THR C C 0.597300 0.597300 -0.131500 1.600000 1.699835 109 THR O O -0.567900 -0.567900 0.029400 1.420000 1.479961 110 GLU N N -0.516300 -0.222700 0.524800 1.450000 1.624999 111 GLU H H 0.293600 0.000000 0.000000 1.100000 0.534539 112 GLU CA CT 0.039700 0.150200 0.485500 1.600000 1.699835 113 GLU HA H1 0.110500 0.000000 0.000000 1.100000 1.235677 114 GLU CB CT 0.056000 0.021400 0.100200 1.600000 1.699835 115 GLU HB2 HC -0.017300 0.000000 0.000000 1.100000 1.324766 116 GLU HB3 HC -0.017300 0.000000 0.000000 1.100000 1.324766 117 GLU CG CT 0.013600 -0.071400 0.755400 1.600000 1.699835 118 GLU HG2 HC -0.042500 0.000000 0.000000 1.100000 1.324766 119 GLU HG3 HC -0.042500 0.000000 0.000000 1.100000 1.324766 120 GLU CD C 0.805400 0.805400 -0.903600 1.600000 1.699835 121 GLU OE1 O2 -0.818800 -0.818800 -0.013400 1.420000 1.479961 122 GLU OE2 O2 -0.818800 -0.818800 -0.013400 1.420000 1.479961 123 GLU C C 0.536600 0.536600 -0.117800 1.600000 1.699835 124 GLU O O -0.581900 -0.581900 -0.045300 1.420000 1.479961 125 GLU N N -0.516300 -0.222700 0.464100 1.450000 1.624999 126 GLU H H 0.293600 0.000000 0.000000 1.100000 0.534539 127 GLU CA CT 0.039700 0.150200 0.485500 1.600000 1.699835 128 GLU HA H1 0.110500 0.000000 0.000000 1.100000 1.235677 129 GLU CB CT 0.056000 0.021400 0.100200 1.600000 1.699835 130 GLU HB2 HC -0.017300 0.000000 0.000000 1.100000 1.324766 131 GLU HB3 HC -0.017300 0.000000 0.000000 1.100000 1.324766 132 GLU CG CT 0.013600 -0.071400 0.755400 1.600000 1.699835 133 GLU HG2 HC -0.042500 0.000000 0.000000 1.100000 1.324766 134 GLU HG3 HC -0.042500 0.000000 0.000000 1.100000 1.324766 135 GLU CD C 0.805400 0.805400 -0.903600 1.600000 1.699835 136 GLU OE1 O2 -0.818800 -0.818800 -0.013400 1.420000 1.479961 137 GLU OE2 O2 -0.818800 -0.818800 -0.013400 1.420000 1.479961 138 GLU C C 0.536600 0.536600 -0.038900 1.600000 1.699835 139 GLU O O -0.581900 -0.581900 -0.045300 1.420000 1.479961 140 ALA N N -0.415700 -0.143800 0.508800 1.450000 1.624999 141 ALA H H 0.271900 0.000000 0.000000 1.100000 0.534539 142 ALA CA CT 0.033700 0.116000 0.567900 1.600000 1.699835 143 ALA HA H1 0.082300 0.000000 0.000000 1.100000 1.235677 144 ALA CB CT -0.182500 -0.001600 0.114400 1.600000 1.699835 145 ALA HB1 HC 0.060300 0.000000 0.000000 1.100000 1.324766 146 ALA HB2 HC 0.060300 0.000000 0.000000 1.100000 1.324766 147 ALA HB3 HC 0.060300 0.000000 0.000000 1.100000 1.324766 148 ALA C C 0.597300 0.597300 0.001600 1.600000 1.699835 149 ALA O O -0.567900 -0.567900 0.029400 1.420000 1.479961 150 LEU N N -0.415700 -0.143800 0.493900 1.450000 1.624999 151 LEU H H 0.271900 0.000000 0.000000 1.100000 0.534539 152 LEU CA CT -0.051800 0.040400 0.475100 1.600000 1.699835 153 LEU HA H1 0.092200 0.000000 0.000000 1.100000 1.235677 154 LEU CB CT -0.110200 -0.018800 0.338600 1.600000 1.699835 155 LEU HB2 HC 0.045700 0.000000 0.000000 1.100000 1.324766 156 LEU HB3 HC 0.045700 0.000000 0.000000 1.100000 1.324766 157 LEU CG CT 0.353100 0.317000 0.074000 1.600000 1.699835 158 LEU HG HC -0.036100 0.000000 0.000000 1.100000 1.324766 159 LEU CD1 CT -0.412100 -0.112100 0.204900 1.600000 1.699835 160 LEU HD11 HC 0.100000 0.000000 0.000000 1.100000 1.324766 161 LEU HD12 HC 0.100000 0.000000 0.000000 1.100000 1.324766 162 LEU HD13 HC 0.100000 0.000000 0.000000 1.100000 1.324766 163 LEU CD2 CT -0.412100 -0.112100 0.204900 1.600000 1.699835 164 LEU HD21 HC 0.100000 0.000000 0.000000 1.100000 1.324766 165 LEU HD22 HC 0.100000 0.000000 0.000000 1.100000 1.324766 166 LEU HD23 HC 0.100000 0.000000 0.000000 1.100000 1.324766 167 LEU C C 0.597300 0.597300 -0.044200 1.600000 1.699835 168 LEU O O -0.567900 -0.567900 0.029400 1.420000 1.479961 169 ALA N N -0.382100 -0.114000 0.415300 1.450000 1.624999 170 ALA H H 0.268100 0.000000 0.000000 1.100000 0.534539 171 ALA CA CT -0.174700 -0.068000 0.611000 1.600000 1.699835 172 ALA HA H1 0.106700 0.000000 0.000000 1.100000 1.235677 173 ALA CB CT -0.209300 0.019900 -0.048100 1.600000 1.699835 174 ALA HB1 HC 0.076400 0.000000 0.000000 1.100000 1.324766 175 ALA HB2 HC 0.076400 0.000000 0.000000 1.100000 1.324766 176 ALA HB3 HC 0.076400 0.000000 0.000000 1.100000 1.324766 177 ALA C C 0.773100 0.773100 -0.905900 1.600000 1.699835 178 ALA O O2 -0.805500 -0.805500 -0.032400 1.420000 1.479961 179 ALA OXT O2 -0.805500 -0.805500 -0.032400 1.420000 1.479961 total system charges (+/-) for PB -1.0000 22.7125 -23.7125 cavity_surften = 0.0436 cavity_offset = -1.0080 SAS Surface: surface dots generated: 366 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- 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 14972 NB-update: atom-based nb list 9199 ======== Setting up Grid Parameters ======== Using bounding box for grid setup Bounding Box Center: 7.000 65.000 114.000 Xmin, Xmax, Xmax-Xmin: -3.759 17.794 21.553 Ymin, Ymax, Ymax-Ymin: 55.004 74.249 19.245 Zmin, Zmax, Zmax-Zmin: 106.134 120.944 14.810 beginning box center at level 1 7.000 65.000 114.000 beginning box center at level 2 7.000 65.000 114.000 Grid dimension at level 1 7 7 7 Grid origin corrected at level 1 -25.000 33.000 82.000 Grid dimension at level 2 41 41 41 Grid origin corrected at level 2 -14.000 44.000 93.000 ======== Setting up Solvent Accessibility Data ======== Setting up working radii Found nonzero radii 179 Number of SA srf points exposed 5780 Number of SA arcs generated 3731 Number of SA arc points exposed 13218 with resolution (A) 0.0625 Atomic solvent accessible surface area: 1 3.90433014866626 2 6.43768986391351 3 19.7422489160014 4 17.1671729704360 5 0.00000000000000 6 6.22310020178306 7 1.23603645387139 8 18.8838902674796 9 10.0857141201312 10 2.16306379427494 11 6.18018226935697 12 8.79817614734847 13 6.79820049629267 14 16.7379936461751 15 13.2873918791175 16 25.7507594556540 17 12.0513554252461 18 25.5361697935236 19 7.10720960976052 20 18.2401212810883 21 0.00000000000000 22 1.63824271596115 23 0.557761449809466 24 9.87112445800072 25 2.47207290774279 26 13.3045590520879 27 20.6006075645232 28 0.00000000000000 29 7.64513267448535 30 0.00000000000000 31 0.00000000000000 32 0.00000000000000 33 0.00000000000000 34 0.00000000000000 35 7.08145885030486 36 6.18018226935697 37 3.21884493195676 38 21.2443765509146 39 2.78966560769585 40 7.72522783669621 41 10.5148934443921 42 21.0297868887841 43 1.71671729704360 44 0.00000000000000 45 0.00000000000000 46 0.00000000000000 47 0.00000000000000 48 0.00000000000000 49 0.429179324260901 50 0.618018226935697 51 6.00851053965261 52 7.08145885030486 53 0.00000000000000 54 1.50212763491315 55 0.927027340403546 56 16.0942246597838 57 12.8753797278270 58 0.214589662130450 59 7.10720960976052 60 11.1586624307834 61 21.6735558751755 62 17.8109419568274 63 0.00000000000000 64 1.09216181064076 65 1.11552289961893 66 2.36048628343495 67 3.09009113467848 68 0.00000000000000 69 21.6735558751755 70 3.09009113467848 71 0.819121357980573 72 0.00000000000000 73 0.00000000000000 74 0.00000000000000 75 2.36048628343495 76 0.618018226935697 77 0.429179324260901 78 14.1629177006097 79 1.54504556733924 80 18.2401212810883 81 8.15440716095711 82 0.618018226935697 83 14.3775073627402 84 17.1671729704360 85 0.00000000000000 86 0.00000000000000 87 3.70810936161418 88 12.5496326207130 89 15.6650453355229 90 24.4632214828713 91 2.23104579923787 92 0.00000000000000 93 21.6735558751755 94 0.618018226935697 95 3.54952588458248 96 0.00000000000000 97 0.00000000000000 98 0.00000000000000 99 4.29179324260901 100 0.00000000000000 101 2.14589662130450 102 2.16306379427494 103 8.79817614734847 104 21.0297868887841 105 3.86261391834811 106 9.01033493778630 107 10.7294831065225 108 0.00000000000000 109 0.00000000000000 110 0.00000000000000 111 0.00000000000000 112 0.00000000000000 113 6.00851053965261 114 0.927027340403546 115 1.93130695917405 116 16.0942246597838 117 0.927027340403546 118 16.9525833083056 119 0.00000000000000 120 2.78108202121064 121 27.8501261713395 122 42.3212701623296 123 0.618018226935697 124 1.36520226330095 125 0.00000000000000 126 0.00000000000000 127 0.00000000000000 128 8.58358648521802 129 0.309009113467848 130 3.43343459408721 131 14.3775073627402 132 1.85405468080709 133 13.9483280384793 134 3.00425526982631 135 5.87117315588912 136 37.1335015617860 137 47.5090387628732 138 0.618018226935697 139 15.0172248963105 140 0.278880724904733 141 0.00000000000000 142 0.00000000000000 143 15.6650453355229 144 6.18018226935697 145 1.07294831065225 146 20.8151972266537 147 14.8066866870011 148 0.00000000000000 149 26.2118834553783 150 0.00000000000000 151 0.00000000000000 152 0.00000000000000 153 5.79392087752216 154 0.618018226935697 155 2.36048628343495 156 8.79817614734847 157 0.00000000000000 158 1.07294831065225 159 5.87117315588912 160 18.8838902674796 161 12.2316107414357 162 7.29604851243531 163 6.79820049629267 164 9.01276580947891 165 21.2443765509146 166 18.4547109432187 167 0.618018226935697 168 18.5667507808930 169 0.00000000000000 170 0.00000000000000 171 0.00000000000000 172 10.5148934443921 173 7.72522783669621 174 12.8753797278270 175 19.9568385781319 176 18.4547109432187 177 3.39910024814633 178 36.3143802038054 179 24.3006002867570 ======== FDPB Summary ======== Do FDPB every 1 steps Nonbonded Update residue cutoff is set to 99.0000000000000 fdpb cutoff is set to 5.00000000000000 sas cutoff is set to 9.00000000000000 nonbonded cutoff is set to 5.00000000000000 Grid Constants Grid dimension 7 7 7 Grid spacing set to 8.00000000000000 Grid boundary -25.000 39.000 33.000 97.000 82.000 146.000 Dielectric Map Use Pymol radii definition for potential surface display Use probe-based SES definition Compute SAS/SAR every 1 steps Solvent probe radius 1.40000000000000 Surface dots per atom 366 Buried atom radii increment 0.800000000000000 Threshhold for exposed atom 0.200000000000000 Current SAS 1350.45411667378 Boundary conditions sum of grid charges as independent DH spheres Physical constants Solute dielectric constant : 1.00000000000000 Solvent dielectric constant : 80.0000000000000 Temperature (K) : 300.000000000000 Ionic strength (mM) : 0.00000000000000 Debye-Huckel parameter (1/A): 0.00000000000000 FD Solver Option Use Modified ICCG solver Iteration data Maximum iterations : 100 Convergence criteria: 1.000000000000000E-003 Iterations required : 6 Norm of the constant vector: 185.609477232325 Norm of the residual vector: 6.974265105394560E-002 Convergence achieved : 3.757494072711035E-004 ======== FDPB Summary ======== Do FDPB every 1 steps Nonbonded Update residue cutoff is set to 99.0000000000000 fdpb cutoff is set to 5.00000000000000 sas cutoff is set to 9.00000000000000 nonbonded cutoff is set to 5.00000000000000 Grid Constants Grid dimension 41 41 41 Grid spacing set to 1.00000000000000 Grid boundary -14.000 28.000 44.000 86.000 93.000 135.000 Dielectric Map Use Pymol radii definition for potential surface display Use probe-based SES definition Compute SAS/SAR every 1 steps Solvent probe radius 1.40000000000000 Surface dots per atom 366 Buried atom radii increment 0.800000000000000 Threshhold for exposed atom 0.200000000000000 Current SAS 1350.45411667378 Boundary conditions electrostatic focus boundary condition Physical constants Solute dielectric constant : 1.00000000000000 Solvent dielectric constant : 80.0000000000000 Temperature (K) : 300.000000000000 Ionic strength (mM) : 0.00000000000000 Debye-Huckel parameter (1/A): 0.00000000000000 FD Solver Option Use Modified ICCG solver Iteration data Maximum iterations : 100 Convergence criteria: 1.000000000000000E-003 Iterations required : 24 Norm of the constant vector: 26712.8194424878 Norm of the residual vector: 24.6244059632691 Convergence achieved : 9.218198032702986E-004 writing potential map in delphi format Total surface charge 0.9871 Reaction field energy -515.1910 NSTEP = 1 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -1281.3887 EKtot = 0.0000 EPtot = 0.0000 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 29.1004 EELEC = -795.2981 EPB = -515.1910 RESTRAINT = 0.0000 ECAVITY= 0.0000 EDISPER = 0.0000 ------------------------------------------------------------------------------ Maximum number of minimization cycles reached. FINAL RESULTS NSTEP = 1 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -1281.3887 EKtot = 0.0000 EPtot = 0.0000 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 29.1004 EELEC = -795.2981 EPB = -515.1910 RESTRAINT = 0.0000 ECAVITY= 0.0000 EDISPER = 0.0000 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Total time 0.91 | Read prm/crd time 0.03 | Force time 0.88 | Nonbond force 0.88 | PB Nonbond 0.88 | PB NB list 0.00 | PB FD grid 0.43 | PB FD Force 0.45 | PB Epsmap 0.13 | PB Solver 0.28 | PB Direct 0.00 | Job began at 13:40:26.113 on 01/01/2004 | Setup done at 13:40:26.142 on 01/01/2004 | Run done at 13:40:27.026 on 01/01/2004 | wallclock() was called 34 times