Mon Oct 10 11:33:09 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+sph.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 = amb.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 Mon Oct 10 2011 at 11:33:09 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2138 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7207645 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): -10.88400 38.39200 ymin,ymax (A): -22.12800 26.83200 zmin,zma (A): -13.22500 36.16700 x,y,z range (A): 49.27600 48.96000 49.39200 scale (grids/A): 0.7207645 object centre (A): 13.75400 2.351999 11.47100 number of atom coordinates read : 2138 total number of charged atoms : 1998 net assigned charge : -5.999980 assigned positive charge : 320.7838 centred at (gu) : 88.17127 88.42393 89.78928 assigned negative charge : -326.7840 centred at (gu) : 87.99878 88.35027 89.97070 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7624 nv = 96 ne = 84 npr = 44043 no. pairs analyzed = 44043 no. exposed pairs = 2730 no. arc points = 19106 no. surface atoms = 920 nbur = 1218 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 523 mr = 4241 m= 5 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 185 time to turn everything in is 0.1800000 number of dielectric boundary points 3822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1622 ## 112 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8197 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0071102E-08 -1.8482598E-07 midg,1,midg; midg,igrid,midg -1.5733163E-07 -1.1907409E-08 1,midg,midg; igrid,midg,midg -2.6556992E-07 3.5117917E-08 gauss-seidel spectral radius is 0.9899753 estimated iterations to convergence 81 setup time was (sec) 0.3700000 now iterating at: 11:33:10 rms-change max change #iterations 0.2194292 27.74118 at 10iterations 2.7883664E-02 3.572117 at 20iterations 3.5377021E-03 0.4720001 at 30iterations 4.5418149E-04 6.0560226E-02 at 40iterations 5.7743004E-05 7.9498291E-03 at 50iterations finished qdiffx linear iterations at : 11:33:12 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 5.7743004E-05 7.9498291E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 11:33:13 3.408u 0.162s 0:04.06 87.6% 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 Mon Oct 10 2011 at 11:33:13 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2138 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.162294 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): -10.88400 38.39200 ymin,ymax (A): -22.12800 26.83200 zmin,zma (A): -13.22500 36.16700 x,y,z range (A): 49.27600 48.96000 49.39200 scale (grids/A): 2.162294 object centre (A): 13.75400 2.351999 11.47100 number of atom coordinates read : 2138 total number of charged atoms : 1998 net assigned charge : -5.999980 assigned positive charge : 320.7838 centred at (gu) : 84.51347 85.27173 89.36775 assigned negative charge : -326.7840 centred at (gu) : 83.99619 85.05074 89.91210 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80425 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19106 grid for indexing accessible points = 1.400000 m= 31252 mr = 55289 m= 6187 mr = 23595 m= 588 mr = 4124 m= 12 mr = 264 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 4759 time to turn everything in is 0.4000000 number of dielectric boundary points 35192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15891 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) : 0.7207645 object centre at (A) : 13.75400 2.351999 11.47100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2439630E-02 -7.7459611E-02 midg,1,midg; midg,igrid,midg -1.5770718E-02 8.7256990E-03 1,midg,midg; igrid,midg,midg -6.0363051E-02 2.9154794E-02 gauss-seidel spectral radius is 0.9988779 estimated iterations to convergence 236 setup time was (sec) 0.6200000 now iterating at: 11:33:14 rms-change max change #iterations 4.904996 182.0583 at 10iterations 2.453685 91.83543 at 20iterations 1.228136 37.42814 at 30iterations 0.6166194 18.95694 at 40iterations 0.3109033 9.197124 at 50iterations 0.1556080 4.642014 at 60iterations 7.8010246E-02 2.191452 at 70iterations 3.9346229E-02 1.167867 at 80iterations 1.9723905E-02 0.5588398 at 90iterations 9.9094333E-03 0.2943954 at 100iterations 4.9773166E-03 0.1533968 at 110iterations 2.4962907E-03 6.9139481E-02 at 120iterations finished qdiffx linear iterations at : 11:33:21 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 2.4962907E-03 6.9139481E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 11:33:22 7.952u 0.208s 0:08.47 96.2% 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 Mon Oct 10 2011 at 11:33:22 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2138 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.243440 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): -10.88400 38.39200 ymin,ymax (A): -22.12800 26.83200 zmin,zma (A): -13.22500 36.16700 x,y,z range (A): 49.27600 48.96000 49.39200 scale (grids/A): 3.243440 object centre (A): 13.75400 2.351999 11.47100 number of atom coordinates read : 2138 total number of charged atoms : 1998 net assigned charge : -5.999980 assigned positive charge : 320.7838 centred at (gu) : 81.77015 82.90754 89.05156 assigned negative charge : -326.7840 centred at (gu) : 80.99429 82.57613 89.86812 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 185116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19106 grid for indexing accessible points = 1.400000 m= 97158 mr = 133294 m= 39856 mr = 80374 m= 11741 mr = 32707 m= 2495 mr = 9132 m= 259 mr = 1803 m= 8 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 16089 time to turn everything in is 1.250000 number of dielectric boundary points 79221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 15984 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) : 2.162294 object centre at (A) : 13.75400 2.351999 11.47100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4618637E-03 -0.6000214 midg,1,midg; midg,igrid,midg -3.5487760E-02 -1.4635032E-02 1,midg,midg; igrid,midg,midg -0.4563069 0.1893388 gauss-seidel spectral radius is 0.9993133 estimated iterations to convergence 301 setup time was (sec) 1.480000 now iterating at: 11:33:23 rms-change max change #iterations 10.77816 486.7664 at 10iterations 6.366258 134.6488 at 20iterations 3.726181 75.42142 at 30iterations 2.195128 43.73038 at 40iterations 1.286897 24.57600 at 50iterations 0.7564675 12.69340 at 60iterations 0.4445609 8.094910 at 70iterations 0.2600897 4.545238 at 80iterations 0.1528072 2.797321 at 90iterations 8.9454487E-02 1.504429 at 100iterations 5.2439027E-02 0.8967638 at 110iterations 3.0722106E-02 0.5169621 at 120iterations 1.8042827E-02 0.3131027 at 130iterations 1.0551319E-02 0.2015114 at 140iterations 6.1940919E-03 0.1086472 at 150iterations 3.6230248E-03 6.0886383E-02 at 160iterations 2.1264292E-03 3.7189484E-02 at 170iterations 1.2450801E-03 2.0919800E-02 at 180iterations finished qdiffx linear iterations at : 11:33:35 total time elapsed so far: 12.98000 # loops : 180 mean,max change (kT/e) : 1.2450801E-03 2.0919800E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 11:33:35 13.111u 0.217s 0:13.59 98.0% 0+0k 0+0io 0pf+0w