Sun Oct 9 12:43:20 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 Sun Oct 9 2011 at 12:43:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2922 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6221818 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): -20.55700 28.95900 ymin,ymax (A): -22.13500 35.08300 zmin,zma (A): -15.70200 37.09200 x,y,z range (A): 49.51600 57.21800 52.79400 scale (grids/A): 0.6221818 object centre (A): 4.201000 6.474000 10.69500 number of atom coordinates read : 2922 total number of charged atoms : 2774 net assigned charge : 6.000020 assigned positive charge : 459.8089 centred at (gu) : 89.76939 90.04134 91.00481 assigned negative charge : -453.8099 centred at (gu) : 89.83551 90.16486 90.93816 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7346 nv = 96 ne = 84 npr = 57575 no. pairs analyzed = 57575 no. exposed pairs = 3756 no. arc points = 25603 no. surface atoms = 1258 nbur = 1664 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 367 mr = 3870 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2300000 number of dielectric boundary points 3819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2657 ## 310 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9127 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1825606E-10 1.3179701E-08 midg,1,midg; midg,igrid,midg 1.5043156E-08 -5.3203819E-09 1,midg,midg; igrid,midg,midg 1.1073210E-08 -3.8163617E-10 gauss-seidel spectral radius is 0.9866441 estimated iterations to convergence 71 setup time was (sec) 0.4200000 now iterating at: 12:43:21 rms-change max change #iterations 0.1370135 17.86596 at 10iterations 1.2946501E-02 1.673460 at 20iterations 1.4154147E-03 0.2066422 at 30iterations 2.2169740E-04 3.8978577E-02 at 40iterations 4.7313657E-05 8.6307526E-03 at 50iterations finished qdiffx linear iterations at : 12:43:23 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 4.7313657E-05 8.6307526E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 12:43:24 3.463u 0.175s 0:03.91 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 Sun Oct 9 2011 at 12:43:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2922 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.866545 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): -20.55700 28.95900 ymin,ymax (A): -22.13500 35.08300 zmin,zma (A): -15.70200 37.09200 x,y,z range (A): 49.51600 57.21800 52.79400 scale (grids/A): 1.866545 object centre (A): 4.201000 6.474000 10.69500 number of atom coordinates read : 2922 total number of charged atoms : 2774 net assigned charge : 6.000020 assigned positive charge : 459.8089 centred at (gu) : 89.30727 90.12315 93.01385 assigned negative charge : -453.8099 centred at (gu) : 89.50600 90.49431 92.81420 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 79346 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25603 grid for indexing accessible points = 1.400000 m= 27486 mr = 54268 m= 3650 mr = 19362 m= 220 mr = 1901 m= 4 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 316 time to turn everything in is 0.4000000 number of dielectric boundary points 35112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 250 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 21775 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) : 0.6221818 object centre at (A) : 4.201000 6.474000 10.69500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6551173E-03 4.1805368E-02 midg,1,midg; midg,igrid,midg 4.0771782E-02 -4.1982722E-02 1,midg,midg; igrid,midg,midg 1.8782146E-02 1.2387047E-02 gauss-seidel spectral radius is 0.9986098 estimated iterations to convergence 213 setup time was (sec) 0.6300000 now iterating at: 12:43:25 rms-change max change #iterations 4.459568 167.0783 at 10iterations 2.071816 66.04311 at 20iterations 0.9621357 31.31946 at 30iterations 0.4488451 16.41143 at 40iterations 0.2089181 6.352936 at 50iterations 9.6936680E-02 3.131165 at 60iterations 4.5272317E-02 1.389198 at 70iterations 2.1165214E-02 0.6821423 at 80iterations 9.9100610E-03 0.3149185 at 90iterations 4.6747983E-03 0.1529541 at 100iterations 2.2338126E-03 8.0009460E-02 at 110iterations 1.0842563E-03 3.7286758E-02 at 120iterations finished qdiffx linear iterations at : 12:43:32 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 1.0842563E-03 3.7286758E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 12:43:32 7.986u 0.194s 0:08.50 96.1% 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 Sun Oct 9 2011 at 12:43:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2922 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.799818 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): -20.55700 28.95900 ymin,ymax (A): -22.13500 35.08300 zmin,zma (A): -15.70200 37.09200 x,y,z range (A): 49.51600 57.21800 52.79400 scale (grids/A): 2.799818 object centre (A): 4.201000 6.474000 10.69500 number of atom coordinates read : 2922 total number of charged atoms : 2774 net assigned charge : 6.000020 assigned positive charge : 459.8089 centred at (gu) : 88.96077 90.18459 94.52055 assigned negative charge : -453.8099 centred at (gu) : 89.25900 90.74128 94.22128 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 183439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25603 grid for indexing accessible points = 1.400000 m= 90866 mr = 132164 m= 30215 mr = 72540 m= 6162 mr = 23076 m= 874 mr = 4103 m= 31 mr = 490 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 1156 time to turn everything in is 1.030000 number of dielectric boundary points 79209 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 22192 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) : 1.866545 object centre at (A) : 4.201000 6.474000 10.69500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2247897E-02 0.6614857 midg,1,midg; midg,igrid,midg 0.4597540 -0.4115214 1,midg,midg; igrid,midg,midg 0.1735943 5.1034465E-02 gauss-seidel spectral radius is 0.9992617 estimated iterations to convergence 290 setup time was (sec) 1.270000 now iterating at: 12:43:34 rms-change max change #iterations 10.84983 363.6490 at 10iterations 6.508037 157.7201 at 20iterations 3.866896 85.48833 at 30iterations 2.283438 47.78268 at 40iterations 1.344041 29.13989 at 50iterations 0.7866694 16.33644 at 60iterations 0.4599071 9.448247 at 70iterations 0.2675574 5.509821 at 80iterations 0.1554102 3.316349 at 90iterations 9.0179197E-02 1.646215 at 100iterations 5.2462164E-02 0.9854126 at 110iterations 3.0458577E-02 0.5648727 at 120iterations 1.7726311E-02 0.3210297 at 130iterations 1.0354511E-02 0.1985435 at 140iterations 6.1049578E-03 0.1302853 at 150iterations 3.6502241E-03 6.7298889E-02 at 160iterations 2.2251231E-03 4.5188904E-02 at 170iterations 1.4027617E-03 3.1906128E-02 at 180iterations finished qdiffx linear iterations at : 12:43:45 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 1.4027617E-03 3.1906128E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 12:43:46 12.892u 0.197s 0:13.35 97.9% 0+0k 0+0io 0pf+0w