Tue Oct 11 03:17:39 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 03:17:39 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5061 !!! WARNING: HIR 53 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: HIT 351 has a net charge of 0.5140 !!! WARNING: NAI 1721 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5344383 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 17.30500 80.12200 ymin,ymax (A): -0.1539999 66.45800 zmin,zma (A): 6.617000 69.29200 x,y,z range (A): 62.81700 66.61200 62.67500 scale (grids/A): 0.5344383 object centre (A): 48.71350 33.15200 37.95450 number of atom coordinates read : 5061 total number of charged atoms : 4952 net assigned charge : 2.542014 assigned positive charge : 789.5667 centred at (gu) : 89.40948 89.97253 90.27207 assigned negative charge : -787.0311 centred at (gu) : 89.43064 89.90639 90.26173 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 9125 nv = 96 ne = 84 npr = 102364 no. pairs analyzed = 102364 no. exposed pairs = 5988 no. arc points = 40943 no. surface atoms = 2010 nbur = 3051 mkacc time = 0.2400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 345 mr = 5061 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 79 time to turn everything in is 0.5200000 number of dielectric boundary points 4398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4069 ## 480 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 12297 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9158900E-11 1.8930936E-10 midg,1,midg; midg,igrid,midg -4.0953838E-10 5.9122046E-10 1,midg,midg; igrid,midg,midg 3.0011638E-10 -5.2744573E-11 gauss-seidel spectral radius is 0.9821065 estimated iterations to convergence 62 setup time was (sec) 0.7700000 now iterating at: 03:17:40 rms-change max change #iterations 9.3410335E-02 13.19395 at 10iterations 6.2668952E-03 0.8321800 at 20iterations 7.0123503E-04 9.1197968E-02 at 30iterations 2.0167571E-04 2.4616241E-02 at 40iterations 6.9218724E-05 8.8148117E-03 at 50iterations finished qdiffx linear iterations at : 03:17:43 total time elapsed so far: 3.660000 # loops : 50 mean,max change (kT/e) : 6.9218724E-05 8.8148117E-03 energy calculations done at 3.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.850000 DelPhi exited at 03:17:44 3.851u 0.193s 0:04.35 92.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 03:17:44 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5061 !!! WARNING: HIR 53 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: HIT 351 has a net charge of 0.5140 !!! WARNING: NAI 1721 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.603315 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 17.30500 80.12200 ymin,ymax (A): -0.1539999 66.45800 zmin,zma (A): 6.617000 69.29200 x,y,z range (A): 62.81700 66.61200 62.67500 scale (grids/A): 1.603315 object centre (A): 48.71350 33.15200 37.95450 number of atom coordinates read : 5061 total number of charged atoms : 4952 net assigned charge : 2.542014 assigned positive charge : 789.5667 centred at (gu) : 88.22665 89.91547 90.81419 assigned negative charge : -787.0311 centred at (gu) : 88.29176 89.71884 90.78477 start vw surface at 0.2400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 103051 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40943 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 32430 mr = 73038 m= 3078 mr = 23080 m= 63 mr = 1417 m= 0 mr = 2 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 3995 time to turn everything in is 0.7600000 number of dielectric boundary points 41085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 387 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 37704 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5344383 object centre at (A) : 48.71350 33.15200 37.95450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8211085E-02 2.0625336E-02 midg,1,midg; midg,igrid,midg -1.7589008E-02 -6.1944067E-03 1,midg,midg; igrid,midg,midg 4.1073305E-03 -5.7475158E-04 gauss-seidel spectral radius is 0.9983189 estimated iterations to convergence 194 setup time was (sec) 1.060000 now iterating at: 03:17:45 rms-change max change #iterations 4.492794 161.2922 at 10iterations 1.937621 57.89381 at 20iterations 0.8364146 29.57018 at 30iterations 0.3607877 10.00524 at 40iterations 0.1554258 4.442745 at 50iterations 6.7243561E-02 2.009395 at 60iterations 2.8978400E-02 0.8543129 at 70iterations 1.2573943E-02 0.3545761 at 80iterations 5.4722936E-03 0.1821632 at 90iterations 2.3958306E-03 6.6773415E-02 at 100iterations 1.0725867E-03 3.3019066E-02 at 110iterations 4.9636810E-04 1.4658451E-02 at 120iterations finished qdiffx linear iterations at : 03:17:52 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 4.9636810E-04 1.4658451E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 03:17:52 8.009u 0.162s 0:08.60 94.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 03:17:53 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5061 !!! WARNING: HIR 53 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: HIT 351 has a net charge of 0.5140 !!! WARNING: NAI 1721 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.404972 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 17.30500 80.12200 ymin,ymax (A): -0.1539999 66.45800 zmin,zma (A): 6.617000 69.29200 x,y,z range (A): 62.81700 66.61200 62.67500 scale (grids/A): 2.404972 object centre (A): 48.71350 33.15200 37.95450 number of atom coordinates read : 5061 total number of charged atoms : 4952 net assigned charge : 2.542014 assigned positive charge : 789.5667 centred at (gu) : 87.33940 89.87272 91.22095 assigned negative charge : -787.0311 centred at (gu) : 87.43732 89.57796 91.17713 start vw surface at 0.2000000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 239731 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40943 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 114313 mr = 178310 m= 31569 mr = 92496 m= 4450 mr = 24102 m= 259 mr = 2799 m= 3 mr = 83 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 13746 time to turn everything in is 1.800000 number of dielectric boundary points 92536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 39548 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.603315 object centre at (A) : 48.71350 33.15200 37.95450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2289461 0.2997213 midg,1,midg; midg,igrid,midg -0.1628981 -0.1811021 1,midg,midg; igrid,midg,midg -1.0634656E-02 -3.2636847E-02 gauss-seidel spectral radius is 0.9992241 estimated iterations to convergence 283 setup time was (sec) 2.150000 now iterating at: 03:17:55 rms-change max change #iterations 11.58993 312.8149 at 10iterations 6.753281 157.0731 at 20iterations 3.911888 78.39864 at 30iterations 2.258386 53.64691 at 40iterations 1.301174 23.83718 at 50iterations 0.7462976 14.98521 at 60iterations 0.4263001 7.326170 at 70iterations 0.2434887 4.787448 at 80iterations 0.1392395 2.319382 at 90iterations 7.9391018E-02 1.375567 at 100iterations 4.5334484E-02 0.8632917 at 110iterations 2.5782349E-02 0.4465828 at 120iterations 1.4719282E-02 0.2393727 at 130iterations 8.3949324E-03 0.1497042 at 140iterations 4.7981036E-03 7.7578664E-02 at 150iterations 2.7507467E-03 5.0718307E-02 at 160iterations 1.5858513E-03 2.8179169E-02 at 170iterations 9.2479284E-04 1.5595436E-02 at 180iterations finished qdiffx linear iterations at : 03:18:07 total time elapsed so far: 13.75000 # loops : 180 mean,max change (kT/e) : 9.2479284E-04 1.5595436E-02 energy calculations done at 13.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.98000 DelPhi exited at 03:18:07 13.980u 0.234s 0:14.58 97.4% 0+0k 0+0io 0pf+0w