Thu Jan 19 13:33:54 PST 2012 #!/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 Thu Jan 19 2012 at 13:33:55 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6831 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4371048 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): -2.365000 79.08000 ymin,ymax (A): -12.14400 67.37600 zmin,zma (A): -23.32600 42.03400 x,y,z range (A): 81.44500 79.52000 65.36000 scale (grids/A): 0.4371048 object centre (A): 38.35750 27.61600 9.354000 number of atom coordinates read : 6831 total number of charged atoms : 6660 net assigned charge : 2.200046 assigned positive charge : 1046.897 centred at (gu) : 88.11127 90.20274 89.98634 assigned negative charge : -1044.706 centred at (gu) : 88.03214 90.26025 89.90457 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7720 nv = 96 ne = 84 npr = 137211 no. pairs analyzed = 137211 no. exposed pairs = 8865 no. arc points = 60737 no. surface atoms = 2952 nbur = 3879 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 = 1.904000 m= 213 mr = 3630 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.4400000 number of dielectric boundary points 4301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5186 ## 1089 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10752 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.1349658E-12 8.5984128E-12 midg,1,midg; midg,igrid,midg 5.9657127E-12 -5.0257793E-12 1,midg,midg; igrid,midg,midg -1.2377752E-11 4.7212325E-12 gauss-seidel spectral radius is 0.9734369 estimated iterations to convergence 51 setup time was (sec) 0.6300000 now iterating at: 13:33:56 rms-change max change #iterations 3.2710843E-02 4.796349 at 10iterations 1.6613773E-03 0.2998562 at 20iterations 4.3322024E-04 5.9059143E-02 at 30iterations 1.5548308E-04 2.0591736E-02 at 40iterations 5.6476332E-05 7.4138641E-03 at 50iterations finished qdiffx linear iterations at : 13:34:06 total time elapsed so far: 3.670000 # loops : 50 mean,max change (kT/e) : 5.6476332E-05 7.4138641E-03 energy calculations done at 3.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.800000 DelPhi exited at 13:34:07 3.806u 0.189s 0:11.95 33.3% 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 Thu Jan 19 2012 at 13:34:07 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6831 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.311314 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): -2.365000 79.08000 ymin,ymax (A): -12.14400 67.37600 zmin,zma (A): -23.32600 42.03400 x,y,z range (A): 81.44500 79.52000 65.36000 scale (grids/A): 1.311314 object centre (A): 38.35750 27.61600 9.354000 number of atom coordinates read : 6831 total number of charged atoms : 6660 net assigned charge : 2.200046 assigned positive charge : 1046.897 centred at (gu) : 84.33165 90.60672 89.95725 assigned negative charge : -1044.706 centred at (gu) : 84.09607 90.78025 89.71328 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 90556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60737 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 20221 mr = 59416 m= 1015 mr = 11684 m= 5 mr = 227 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 630 time to turn everything in is 0.4700000 number of dielectric boundary points 40470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1216 ## 53 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 46664 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) : 0.4371048 object centre at (A) : 38.35750 27.61600 9.354000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8842116E-03 2.5482264E-03 midg,1,midg; midg,igrid,midg 8.6095482E-03 4.0133521E-03 1,midg,midg; igrid,midg,midg -1.7102819E-02 3.5749241E-03 gauss-seidel spectral radius is 0.9975095 estimated iterations to convergence 160 setup time was (sec) 0.7100000 now iterating at: 13:34:08 rms-change max change #iterations 3.241344 171.4484 at 10iterations 1.161718 46.90763 at 20iterations 0.4166554 13.98765 at 30iterations 0.1497801 4.728115 at 40iterations 5.4046985E-02 1.773880 at 50iterations 1.9461993E-02 0.7361321 at 60iterations 7.1437764E-03 0.2469292 at 70iterations 2.7075915E-03 0.1066484 at 80iterations 1.1296246E-03 3.7618160E-02 at 90iterations 5.6390162E-04 1.9005060E-02 at 100iterations 3.3877944E-04 1.0531902E-02 at 110iterations 2.2242569E-04 6.1416626E-03 at 120iterations finished qdiffx linear iterations at : 13:34:30 total time elapsed so far: 8.080000 # loops : 120 mean,max change (kT/e) : 2.2242569E-04 6.1416626E-03 energy calculations done at 8.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.220000 DelPhi exited at 13:34:31 8.218u 0.213s 0:24.34 34.5% 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 Thu Jan 19 2012 at 13:34:31 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6831 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.966972 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): -2.365000 79.08000 ymin,ymax (A): -12.14400 67.37600 zmin,zma (A): -23.32600 42.03400 x,y,z range (A): 81.44500 79.52000 65.36000 scale (grids/A): 1.966972 object centre (A): 38.35750 27.61600 9.354000 number of atom coordinates read : 6831 total number of charged atoms : 6660 net assigned charge : 2.200046 assigned positive charge : 1046.897 centred at (gu) : 81.49702 90.90961 89.93553 assigned negative charge : -1044.706 centred at (gu) : 81.14415 91.17035 89.56991 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 212366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60737 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 80123 mr = 148688 m= 13535 mr = 58328 m= 1008 mr = 8311 m= 21 mr = 415 m= 0 mr = 0 time to grow re-entrant surface = 0.5799999 no. cavity mid-points inaccessible to solvent = 2019 time to turn everything in is 1.070000 number of dielectric boundary points 91311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 371 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 52652 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) : 1.311314 object centre at (A) : 38.35750 27.61600 9.354000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2384525E-02 6.5276213E-02 midg,1,midg; midg,igrid,midg 0.2653787 0.1067297 1,midg,midg; igrid,midg,midg -0.5800353 0.1250670 gauss-seidel spectral radius is 0.9990208 estimated iterations to convergence 253 setup time was (sec) 1.330000 now iterating at: 13:34:34 rms-change max change #iterations 9.837067 288.9825 at 10iterations 5.399551 128.7580 at 20iterations 2.946683 73.22771 at 30iterations 1.591846 39.03916 at 40iterations 0.8546001 20.25632 at 50iterations 0.4586301 10.92269 at 60iterations 0.2458047 5.344740 at 70iterations 0.1307164 3.080628 at 80iterations 6.9723524E-02 1.605816 at 90iterations 3.7149783E-02 0.8122883 at 100iterations 1.9721862E-02 0.4248238 at 110iterations 1.0458617E-02 0.2229919 at 120iterations 5.5549671E-03 0.1179295 at 130iterations 2.9510183E-03 7.1933746E-02 at 140iterations 1.5666507E-03 3.4149170E-02 at 150iterations 8.3368970E-04 1.8508911E-02 at 160iterations 4.4591149E-04 8.7509155E-03 at 170iterations 2.3999598E-04 5.4512024E-03 at 180iterations finished qdiffx linear iterations at : 13:34:58 total time elapsed so far: 13.47000 # loops : 180 mean,max change (kT/e) : 2.3999598E-04 5.4512024E-03 energy calculations done at 13.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.60000 DelPhi exited at 13:34:59 13.600u 0.255s 0:27.50 50.3% 0+0k 0+0io 0pf+0w