------------------------------------------------------- PBSA VERSION 2009 UC Irvine ------------------------------------------------------- | Run on 01/01/2004 at 05:46:48 [-O]verwriting output File Assignments: | MDIN: ESP_pb.in | MDOUT: ESP_pb.out |INPCRD: ESP_test1.inpcrd | PARM: ESP_test1.prmtop | Here is the input file: Sample of PB visualization input &cntrl ntx=1 imin=1 ipb=1 inp=0 / &pb npbverb=1, istrng=0, espout=80, espin=1, space=1, accept=1, sprob=1.4, cutnb=9, phiout=1, phiform=2 / PB Info in pb_read(): npopt has been overwritten with inp -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 01/01/04 Time = 09:15:20 NATOM = 91 NTYPES = 11 NBONH = 46 MBONA = 44 NTHETH = 103 MTHETA = 58 NPHIH = 188 MPHIA = 140 NHPARM = 0 NPARM = 0 NNB = 480 NRES = 6 NBONA = 44 NTHETA = 58 NPHIA = 140 NUMBND = 15 NUMANG = 33 NPTRA = 29 NATYP = 13 NPHB = 0 IFBOX = 0 NMXRS = 19 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 3405 | Hollerith 554 | Integer 22050 | Max Pairs 1 | Max Rstack 1 | Max Istack 1 | Total 114 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: 4141 4141 4141 no. of atoms processed in PB initialization: 91 NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI 1 ALA N N3 0.141400 0.740500 0.925600 1.450000 1.624999 2 ALA H1 H 0.199700 0.000000 0.000000 1.100000 0.534539 3 ALA H2 H 0.199700 0.000000 0.000000 1.100000 0.534539 4 ALA H3 H 0.199700 0.000000 0.000000 1.100000 0.534539 5 ALA CA CT 0.096200 0.185100 1.572200 1.600000 1.699835 6 ALA HA HP 0.088900 0.000000 0.000000 1.100000 0.979989 7 ALA CB CT -0.059700 0.030300 0.215400 1.600000 1.699835 8 ALA HB1 HC 0.030000 0.000000 0.000000 1.100000 1.324766 9 ALA HB2 HC 0.030000 0.000000 0.000000 1.100000 1.324766 10 ALA HB3 HC 0.030000 0.000000 0.000000 1.100000 1.324766 11 ALA C C 0.616300 0.616300 0.085400 1.600000 1.699835 12 ALA O O -0.572200 -0.572200 0.044100 1.420000 1.479961 13 ASN N N -0.415700 -0.143800 0.591600 1.450000 1.624999 14 ASN H H 0.271900 0.000000 0.000000 1.100000 0.534539 15 ASN CA CT 0.014300 0.119100 0.527900 1.600000 1.699835 16 ASN HA H1 0.104800 0.000000 0.000000 1.100000 1.235677 17 ASN CB CT -0.204100 -0.044700 0.787400 1.600000 1.699835 18 ASN HB2 HC 0.079700 0.000000 0.000000 1.100000 1.324766 19 ASN HB3 HC 0.079700 0.000000 0.000000 1.100000 1.324766 20 ASN CG C 0.713000 0.713000 -0.004700 1.600000 1.699835 21 ASN OD1 O -0.593100 -0.593100 0.119900 1.420000 1.479961 22 ASN ND2 N -0.919100 -0.079900 0.633100 1.450000 1.624999 23 ASN HD21 H 0.419600 0.000000 0.000000 1.100000 0.534539 24 ASN HD22 H 0.419600 0.000000 0.000000 1.100000 0.534539 25 ASN C C 0.597300 0.597300 0.004700 1.600000 1.699835 26 ASN O O -0.567900 -0.567900 0.029400 1.420000 1.479961 27 MET N N -0.415700 -0.143800 0.517800 1.450000 1.624999 28 MET H H 0.271900 0.000000 0.000000 1.100000 0.534539 29 MET CA CT -0.023700 0.064300 0.600200 1.600000 1.699835 30 MET HA H1 0.088000 0.000000 0.000000 1.100000 1.235677 31 MET CB CT 0.034200 0.082400 0.236500 1.600000 1.699835 32 MET HB2 HC 0.024100 0.000000 0.000000 1.100000 1.324766 33 MET HB3 HC 0.024100 0.000000 0.000000 1.100000 1.324766 34 MET CG CT 0.001800 0.089800 -0.101500 1.600000 1.699835 35 MET HG2 H1 0.044000 0.000000 0.000000 1.100000 1.235677 36 MET HG3 H1 0.044000 0.000000 0.000000 1.100000 1.235677 37 MET SD S -0.273700 -0.273700 -0.032300 1.700000 1.781797 38 MET CE CT -0.053600 0.151600 -0.122100 1.600000 1.699835 39 MET HE1 H1 0.068400 0.000000 0.000000 1.100000 1.235677 40 MET HE2 H1 0.068400 0.000000 0.000000 1.100000 1.235677 41 MET HE3 H1 0.068400 0.000000 0.000000 1.100000 1.235677 42 MET C C 0.597300 0.597300 -0.050100 1.600000 1.699835 43 MET O O -0.567900 -0.567900 0.029400 1.420000 1.479961 44 ILE N N -0.415700 -0.143800 0.480700 1.450000 1.624999 45 ILE H H 0.271900 0.000000 0.000000 1.100000 0.534539 46 ILE CA CT -0.059700 0.027200 0.629700 1.600000 1.699835 47 ILE HA H1 0.086900 0.000000 0.000000 1.100000 1.235677 48 ILE CB CT 0.130300 0.149000 0.124600 1.600000 1.699835 49 ILE HB HC 0.018700 0.000000 0.000000 1.100000 1.324766 50 ILE CG2 CT -0.320400 -0.055800 0.093200 1.600000 1.699835 51 ILE HG21 HC 0.088200 0.000000 0.000000 1.100000 1.324766 52 ILE HG22 HC 0.088200 0.000000 0.000000 1.100000 1.324766 53 ILE HG23 HC 0.088200 0.000000 0.000000 1.100000 1.324766 54 ILE CG1 CT -0.043000 0.004200 0.143000 1.600000 1.699835 55 ILE HG12 HC 0.023600 0.000000 0.000000 1.100000 1.324766 56 ILE HG13 HC 0.023600 0.000000 0.000000 1.100000 1.324766 57 ILE CD1 CT -0.066000 -0.010200 -0.006000 1.600000 1.699835 58 ILE HD11 HC 0.018600 0.000000 0.000000 1.100000 1.324766 59 ILE HD12 HC 0.018600 0.000000 0.000000 1.100000 1.324766 60 ILE HD13 HC 0.018600 0.000000 0.000000 1.100000 1.324766 61 ILE C C 0.597300 0.597300 -0.087200 1.600000 1.699835 62 ILE O O -0.567900 -0.567900 0.029400 1.420000 1.479961 63 SER N N -0.415700 -0.143800 0.512900 1.450000 1.624999 64 SER H H 0.271900 0.000000 0.000000 1.100000 0.534539 65 SER CA CT -0.024900 0.059400 0.795000 1.600000 1.699835 66 SER HA H1 0.084300 0.000000 0.000000 1.100000 1.235677 67 SER CB CT 0.211700 0.282100 0.114400 1.600000 1.699835 68 SER HB2 H1 0.035200 0.000000 0.000000 1.100000 1.235677 69 SER HB3 H1 0.035200 0.000000 0.000000 1.100000 1.235677 70 SER OG OH -0.654600 -0.227100 0.055000 1.420000 1.533237 71 SER HG HO 0.427500 0.000000 0.000000 1.100000 0.000000 72 SER C C 0.597300 0.597300 -0.025200 1.600000 1.699835 73 SER O O -0.567900 -0.567900 0.029400 1.420000 1.479961 74 GLN N N -0.382100 -0.114000 0.381700 1.450000 1.624999 75 GLN H H 0.268100 0.000000 0.000000 1.100000 0.534539 76 GLN CA CT -0.224800 -0.101600 0.585900 1.600000 1.699835 77 GLN HA H1 0.123200 0.000000 0.000000 1.100000 1.235677 78 GLN CB CT -0.066400 0.024000 -0.058000 1.600000 1.699835 79 GLN HB2 HC 0.045200 0.000000 0.000000 1.100000 1.324766 80 GLN HB3 HC 0.045200 0.000000 0.000000 1.100000 1.324766 81 GLN CG CT -0.021000 0.019600 0.752900 1.600000 1.699835 82 GLN HG2 HC 0.020300 0.000000 0.000000 1.100000 1.324766 83 GLN HG3 HC 0.020300 0.000000 0.000000 1.100000 1.324766 84 GLN CD C 0.709300 0.709300 0.022500 1.600000 1.699835 85 GLN OE1 O -0.609800 -0.609800 0.099500 1.420000 1.479961 86 GLN NE2 N -0.957400 -0.096600 0.612700 1.450000 1.624999 87 GLN HE21 H 0.430400 0.000000 0.000000 1.100000 0.534539 88 GLN HE22 H 0.430400 0.000000 0.000000 1.100000 0.534539 89 GLN C C 0.777500 0.777500 -0.932500 1.600000 1.699835 90 GLN O O2 -0.804200 -0.804200 -0.026700 1.420000 1.479961 91 GLN OXT O2 -0.804200 -0.804200 -0.026700 1.420000 1.479961 total system charges (+/-) for PB 0.0000 11.6721 -11.6721 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 3621 NB-update: atom-based nb list 3502 ======== Setting up Grid Parameters ======== Using bounding box for grid setup Bounding Box Center: 25.000 68.000 3.000 Xmin, Xmax, Xmax-Xmin: 17.929 32.051 14.123 Ymin, Ymax, Ymax-Ymin: 60.960 75.279 14.318 Zmin, Zmax, Zmax-Zmin: -4.032 10.271 14.303 beginning box center at level 1 25.000 68.000 3.000 beginning box center at level 2 25.000 68.000 3.000 Grid dimension at level 1 5 5 5 Grid origin corrected at level 1 1.000 44.000 -21.000 Grid dimension at level 2 33 33 33 Grid origin corrected at level 2 8.000 51.000 -14.000 PB Bomb in setgrd(): focusing grid too large 2 automatically increased fillratio to 3.000 Grid dimension at level 1 7 7 7 Grid origin corrected at level 1 -7.000 36.000 -29.000 Grid dimension at level 2 33 33 33 Grid origin corrected at level 2 8.000 51.000 -14.000 ======== Setting up Solvent Accessibility Data ======== Setting up working radii Found nonzero radii 91 Number of SA srf points exposed 3747 Number of SA arcs generated 1542 Number of SA arc points exposed 7897 with resolution (A) 0.0625 Atomic solvent accessible surface area: 1 1.39440362452367 2 4.07720358047856 3 9.44194513373982 4 18.0255316189578 5 0.00000000000000 6 12.8753797278270 7 8.03423695016406 8 20.1714282402623 9 18.8838902674796 10 22.7465041858277 11 0.00000000000000 12 21.0241148548347 13 0.00000000000000 14 0.00000000000000 15 0.00000000000000 16 4.93556222900036 17 0.618018226935697 18 14.3775073627402 19 10.5148934443921 20 4.63513670201773 21 24.8466811920774 22 13.1073940705225 23 27.6820664148281 24 22.9610938479582 25 0.00000000000000 26 1.91128316862134 27 0.00000000000000 28 3.43343459408721 29 0.00000000000000 30 2.14589662130450 31 0.00000000000000 32 9.65653479587027 33 7.08145885030486 34 0.618018226935697 35 15.0212763491315 36 9.87112445800072 37 40.5842269324890 38 9.27027340403546 39 19.5276592538710 40 25.3215801313931 41 21.8881455373059 42 0.00000000000000 43 8.46425403246592 44 0.00000000000000 45 0.00000000000000 46 0.00000000000000 47 4.72097256686991 48 0.00000000000000 49 3.21884493195676 50 7.10720960976052 51 11.8024314171748 52 20.8151972266537 53 12.4462004035661 54 1.23603645387139 55 7.93981749882666 56 17.1671729704360 57 8.03423695016406 58 8.15440716095711 59 25.3215801313931 60 15.2358660112620 61 0.00000000000000 62 16.1093867069513 63 0.278880724904733 64 0.00000000000000 65 0.00000000000000 66 14.3775073627402 67 1.54504556733924 68 6.00851053965261 69 21.4589662130450 70 9.28337539044649 71 9.44194513373982 72 0.927027340403546 73 27.8501261713395 74 0.00000000000000 75 0.00000000000000 76 0.00000000000000 77 5.79392087752216 78 0.00000000000000 79 0.643768986391351 80 3.64802425621766 81 2.78108202121064 82 15.2358660112620 83 11.5878417550443 84 5.56216404242127 85 34.6761374878442 86 9.76082537166566 87 27.6820664148281 88 22.3173248615668 89 0.927027340403546 90 36.5874206564656 91 19.6589125915337 ======== 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 9.00000000000000 Grid Constants Grid dimension 7 7 7 Grid spacing set to 8.00000000000000 Grid boundary -7.000 57.000 36.000 100.000 -29.000 35.000 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 882.491285188216 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: 1.00000000000000 Iterations required : 1 Norm of the constant vector: 42.8001220029462 Norm of the residual vector: 18.3699424808117 Convergence achieved : 0.429203040111595 ======== 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 9.00000000000000 Grid Constants Grid dimension 33 33 33 Grid spacing set to 1.00000000000000 Grid boundary 8.000 42.000 51.000 85.000 -14.000 20.000 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 882.491285188216 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: 1.00000000000000 Iterations required : 1 Norm of the constant vector: 12615.7039183406 Norm of the residual vector: 2315.27736122458 Convergence achieved : 0.183523438423332 Total surface charge 0.4091 Reaction field energy -245.1391 NSTEP = 1 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -572.2576 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 = -17.4039 EELEC = -309.7145 EPB = -245.1391 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 = -572.2576 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 = -17.4039 EELEC = -309.7145 EPB = -245.1391 RESTRAINT = 0.0000 ECAVITY= 0.0000 EDISPER = 0.0000 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Total time 0.31 | Read prm/crd time 0.02 | Force time 0.29 | Nonbond force 0.29 | PB Nonbond 0.29 | PB FD grid 0.18 | PB FD Force 0.11 | PB Epsmap 0.08 | PB Solver 0.03 | PB Direct 0.00 | Job began at 05:46:48.719 on 01/01/2004 | Setup done at 05:46:48.737 on 01/01/2004 | Run done at 05:46:49.028 on 01/01/2004 | wallclock() was called 34 times