Sat Oct 8 18:26:58 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 Sat Oct 8 2011 at 18:26:58 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 = 3409 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5682091 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): 50.53900 110.5180 ymin,ymax (A): -19.16300 41.60100 zmin,zma (A): -34.58900 28.06400 x,y,z range (A): 59.97900 60.76400 62.65300 scale (grids/A): 0.5682091 object centre (A): 80.52850 11.21900 -3.262499 number of atom coordinates read : 3409 total number of charged atoms : 3266 net assigned charge : 5.000032 assigned positive charge : 509.5944 centred at (gu) : 88.52437 89.43592 90.90672 assigned negative charge : -504.5958 centred at (gu) : 88.48174 89.55649 90.88899 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7327 nv = 96 ne = 84 npr = 67911 no. pairs analyzed = 67911 no. exposed pairs = 4488 no. arc points = 32197 no. surface atoms = 1498 nbur = 1911 mkacc time = 0.1500000 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 = 1.512000 m= 364 mr = 3721 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.3700000 number of dielectric boundary points 3945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3215 ## 370 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9404 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4097586E-10 1.2501536E-09 midg,1,midg; midg,igrid,midg 3.0915048E-09 -1.1566172E-09 1,midg,midg; igrid,midg,midg -2.1328894E-11 1.0058304E-09 gauss-seidel spectral radius is 0.9840622 estimated iterations to convergence 65 setup time was (sec) 0.6200000 now iterating at: 18:26:59 rms-change max change #iterations 9.4441161E-02 13.38842 at 10iterations 7.1511087E-03 1.253304 at 20iterations 6.3383277E-04 9.1362000E-02 at 30iterations 9.0557471E-05 1.2504578E-02 at 40iterations 1.8785973E-05 2.6016235E-03 at 50iterations finished qdiffx linear iterations at : 18:27:01 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.8785973E-05 2.6016235E-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) 3.440000 DelPhi exited at 18:27:02 3.440u 0.172s 0:04.09 88.2% 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 Sat Oct 8 2011 at 18:27:02 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 = 3409 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.704627 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): 50.53900 110.5180 ymin,ymax (A): -19.16300 41.60100 zmin,zma (A): -34.58900 28.06400 x,y,z range (A): 59.97900 60.76400 62.65300 scale (grids/A): 1.704627 object centre (A): 80.52850 11.21900 -3.262499 number of atom coordinates read : 3409 total number of charged atoms : 3266 net assigned charge : 5.000032 assigned positive charge : 509.5944 centred at (gu) : 85.57216 88.30663 92.71911 assigned negative charge : -504.5958 centred at (gu) : 85.44506 88.66935 92.66644 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 79476 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32197 grid for indexing accessible points = 1.400000 m= 27073 mr = 52652 m= 3570 mr = 18743 m= 113 mr = 1951 m= 3 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 2229 time to turn everything in is 0.5900000 number of dielectric boundary points 36886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 272 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 25226 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) : 0.5682091 object centre at (A) : 80.52850 11.21900 -3.262499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0002751E-02 2.1016719E-02 midg,1,midg; midg,igrid,midg 1.3247186E-02 -1.1908931E-02 1,midg,midg; igrid,midg,midg -4.4891373E-03 3.1905668E-03 gauss-seidel spectral radius is 0.9983907 estimated iterations to convergence 198 setup time was (sec) 0.8900000 now iterating at: 18:27:03 rms-change max change #iterations 3.913464 153.3556 at 10iterations 1.706933 61.52930 at 20iterations 0.7486036 23.04424 at 30iterations 0.3277120 10.79313 at 40iterations 0.1435306 5.049322 at 50iterations 6.2711723E-02 2.058268 at 60iterations 2.7567469E-02 0.9253883 at 70iterations 1.2059624E-02 0.4013915 at 80iterations 5.2966075E-03 0.1613321 at 90iterations 2.3453061E-03 8.1905365E-02 at 100iterations 1.0281459E-03 3.2058716E-02 at 110iterations 4.5181575E-04 1.5592694E-02 at 120iterations finished qdiffx linear iterations at : 18:27:10 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 4.5181575E-04 1.5592694E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 18:27:10 7.726u 0.229s 0:08.22 96.5% 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 Sat Oct 8 2011 at 18:27:10 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 = 3409 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.556941 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): 50.53900 110.5180 ymin,ymax (A): -19.16300 41.60100 zmin,zma (A): -34.58900 28.06400 x,y,z range (A): 59.97900 60.76400 62.65300 scale (grids/A): 2.556941 object centre (A): 80.52850 11.21900 -3.262499 number of atom coordinates read : 3409 total number of charged atoms : 3266 net assigned charge : 5.000032 assigned positive charge : 509.5944 centred at (gu) : 83.35808 87.45969 94.07830 assigned negative charge : -504.5958 centred at (gu) : 83.16740 88.00402 93.99969 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 183837 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32197 grid for indexing accessible points = 1.400000 m= 88774 mr = 128677 m= 29897 mr = 69758 m= 6007 mr = 22996 m= 453 mr = 4136 m= 6 mr = 186 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 7701 time to turn everything in is 1.440000 number of dielectric boundary points 83221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 26115 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) : 1.704627 object centre at (A) : 80.52850 11.21900 -3.262499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1627566 -5.3953521E-02 midg,1,midg; midg,igrid,midg 0.1781221 -0.1762692 1,midg,midg; igrid,midg,midg 0.1516375 1.4528666E-03 gauss-seidel spectral radius is 0.9992139 estimated iterations to convergence 282 setup time was (sec) 1.760000 now iterating at: 18:27:12 rms-change max change #iterations 9.978958 330.8712 at 10iterations 5.870878 143.0834 at 20iterations 3.399152 81.99055 at 30iterations 1.961589 45.51184 at 40iterations 1.128705 21.94806 at 50iterations 0.6460292 13.16290 at 60iterations 0.3680870 7.576088 at 70iterations 0.2096184 4.058640 at 80iterations 0.1190941 2.389635 at 90iterations 6.7633949E-02 1.265877 at 100iterations 3.8398266E-02 0.7033982 at 110iterations 2.1732155E-02 0.4003792 at 120iterations 1.2310918E-02 0.2404022 at 130iterations 6.9790818E-03 0.1240416 at 140iterations 3.9407322E-03 7.2858810E-02 at 150iterations 2.2337246E-03 4.4105530E-02 at 160iterations 1.2621727E-03 2.1206856E-02 at 170iterations 7.1339245E-04 1.3122559E-02 at 180iterations finished qdiffx linear iterations at : 18:27:23 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 7.1339245E-04 1.3122559E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.83000 DelPhi exited at 18:27:24 12.833u 0.317s 0:13.49 97.4% 0+0k 0+0io 0pf+0w