Mon Oct 10 11:33:54 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 11:33:54 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 = 2139 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: 0.7154341 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): -22.09600 23.23700 ymin,ymax (A): 7.814000 49.51800 zmin,zma (A): -24.32600 25.43400 x,y,z range (A): 45.33300 41.70400 49.76000 scale (grids/A): 0.7154341 object centre (A): 0.5705004 28.66600 0.5539999 number of atom coordinates read : 2139 total number of charged atoms : 1999 net assigned charge : -5.999980 assigned positive charge : 320.7838 centred at (gu) : 89.32205 90.97463 91.00639 assigned negative charge : -326.7840 centred at (gu) : 89.46864 90.84906 90.84043 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7351 nv = 96 ne = 84 npr = 44469 no. pairs analyzed = 44469 no. exposed pairs = 2679 no. arc points = 19020 no. surface atoms = 896 nbur = 1243 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 445 mr = 4015 m= 5 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 131 time to turn everything in is 0.2600000 number of dielectric boundary points 3724 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1592 ## 120 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8070 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3798305E-07 4.6529681E-08 midg,1,midg; midg,igrid,midg -1.1765498E-07 1.6824218E-08 1,midg,midg; igrid,midg,midg 3.0047538E-08 -1.3615741E-07 gauss-seidel spectral radius is 0.9898254 estimated iterations to convergence 81 setup time was (sec) 0.5600000 now iterating at: 11:33:55 rms-change max change #iterations 0.2158624 34.47802 at 10iterations 2.6828872E-02 3.853738 at 20iterations 3.3851513E-03 0.4692764 at 30iterations 4.2086924E-04 5.7037354E-02 at 40iterations 5.3706102E-05 6.6900253E-03 at 50iterations finished qdiffx linear iterations at : 11:33:58 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 5.3706102E-05 6.6900253E-03 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 11:33:59 4.557u 0.429s 0:05.25 94.6% 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 11:33:59 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 = 2139 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: 2.146302 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): -22.09600 23.23700 ymin,ymax (A): 7.814000 49.51800 zmin,zma (A): -24.32600 25.43400 x,y,z range (A): 45.33300 41.70400 49.76000 scale (grids/A): 2.146302 object centre (A): 0.5705004 28.66600 0.5539999 number of atom coordinates read : 2139 total number of charged atoms : 1999 net assigned charge : -5.999980 assigned positive charge : 320.7838 centred at (gu) : 87.96626 92.92402 93.01889 assigned negative charge : -326.7840 centred at (gu) : 88.40598 92.54731 92.52119 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19020 grid for indexing accessible points = 1.400000 m= 29585 mr = 53169 m= 5881 mr = 22163 m= 545 mr = 3945 m= 14 mr = 250 m= 0 mr = 2 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 3759 time to turn everything in is 0.6300000 number of dielectric boundary points 34203 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 15893 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) : 0.7154341 object centre at (A) : 0.5705004 28.66600 0.5539999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6153289E-02 -3.5284061E-02 midg,1,midg; midg,igrid,midg -3.5082012E-02 -2.6470767E-02 1,midg,midg; igrid,midg,midg 2.4686484E-02 -1.1374416E-02 gauss-seidel spectral radius is 0.9988636 estimated iterations to convergence 235 setup time was (sec) 0.9600000 now iterating at: 11:34:00 rms-change max change #iterations 4.826721 205.6110 at 10iterations 2.399518 97.33628 at 20iterations 1.200236 35.59274 at 30iterations 0.5971367 17.41822 at 40iterations 0.2981943 9.218140 at 50iterations 0.1497108 4.991948 at 60iterations 7.4597701E-02 2.129036 at 70iterations 3.7418500E-02 1.103964 at 80iterations 1.8697681E-02 0.6100416 at 90iterations 9.3571125E-03 0.2798729 at 100iterations 4.6852813E-03 0.1397972 at 110iterations 2.3434469E-03 6.9266319E-02 at 120iterations finished qdiffx linear iterations at : 11:34:10 total time elapsed so far: 10.83000 # loops : 120 mean,max change (kT/e) : 2.3434469E-03 6.9266319E-02 energy calculations done at 10.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.99000 DelPhi exited at 11:34:11 10.996u 0.469s 0:11.81 96.9% 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 11:34:11 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 = 2139 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: 3.219453 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): -22.09600 23.23700 ymin,ymax (A): 7.814000 49.51800 zmin,zma (A): -24.32600 25.43400 x,y,z range (A): 45.33300 41.70400 49.76000 scale (grids/A): 3.219453 object centre (A): 0.5705004 28.66600 0.5539999 number of atom coordinates read : 2139 total number of charged atoms : 1999 net assigned charge : -5.999980 assigned positive charge : 320.7838 centred at (gu) : 86.94934 94.38606 94.52831 assigned negative charge : -326.7840 centred at (gu) : 87.60901 93.82103 93.78185 start vw surface at 0.1100000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 178981 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19020 grid for indexing accessible points = 1.400000 m= 92214 mr = 128417 m= 37423 mr = 75733 m= 11108 mr = 30720 m= 2238 mr = 8590 m= 263 mr = 1604 m= 5 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 12838 time to turn everything in is 2.010000 number of dielectric boundary points 77026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 15992 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) : 2.146302 object centre at (A) : 0.5705004 28.66600 0.5539999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7961493 -0.2592672 midg,1,midg; midg,igrid,midg -0.2322805 -0.2594378 1,midg,midg; igrid,midg,midg 0.1403222 -5.8423091E-02 gauss-seidel spectral radius is 0.9993030 estimated iterations to convergence 299 setup time was (sec) 2.340000 now iterating at: 11:34:14 rms-change max change #iterations 10.66311 396.4820 at 10iterations 6.242913 122.5709 at 20iterations 3.655345 73.12571 at 30iterations 2.136273 38.60255 at 40iterations 1.248948 21.76772 at 50iterations 0.7281821 12.66329 at 60iterations 0.4255313 6.972290 at 70iterations 0.2486264 4.004223 at 80iterations 0.1446131 2.367021 at 90iterations 8.4469736E-02 1.354839 at 100iterations 4.9322490E-02 0.8121901 at 110iterations 2.8722892E-02 0.4925561 at 120iterations 1.6749505E-02 0.2854382 at 130iterations 9.7986646E-03 0.1645889 at 140iterations 5.7073268E-03 0.1007614 at 150iterations 3.3273378E-03 6.3024521E-02 at 160iterations 1.9449830E-03 3.1466484E-02 at 170iterations 1.1342054E-03 2.0061493E-02 at 180iterations finished qdiffx linear iterations at : 11:34:35 total time elapsed so far: 23.68000 # loops : 180 mean,max change (kT/e) : 1.1342054E-03 2.0061493E-02 energy calculations done at 23.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.86000 DelPhi exited at 11:34:36 23.867u 0.656s 0:24.99 98.0% 0+0k 0+0io 0pf+0w