Mon Oct 10 19:35:10 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+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 Mon Oct 10 2011 at 19:35:10 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 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: 0.6389318 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): -12.10600 40.68000 ymin,ymax (A): -28.45500 23.72300 zmin,zma (A): -9.321000 46.39700 x,y,z range (A): 52.78600 52.17800 55.71800 scale (grids/A): 0.6389318 object centre (A): 14.28700 -2.366000 18.53800 number of atom coordinates read : 2734 total number of charged atoms : 2597 net assigned charge : -1.999976 assigned positive charge : 409.9195 centred at (gu) : 89.99415 89.31904 90.58190 assigned negative charge : -411.9207 centred at (gu) : 90.01579 89.28252 90.68929 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7599 nv = 96 ne = 84 npr = 55347 no. pairs analyzed = 55347 no. exposed pairs = 3723 no. arc points = 25969 no. surface atoms = 1233 nbur = 1501 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 452 mr = 3906 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3300000 number of dielectric boundary points 4090 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2499 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9007 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8456655E-09 -1.7882853E-08 midg,1,midg; midg,igrid,midg -8.2241378E-09 1.4249290E-09 1,midg,midg; igrid,midg,midg -1.0269799E-10 -5.2975349E-09 gauss-seidel spectral radius is 0.9873304 estimated iterations to convergence 73 setup time was (sec) 0.6700000 now iterating at: 19:35:11 rms-change max change #iterations 0.1517207 23.70289 at 10iterations 1.4993762E-02 2.227893 at 20iterations 1.5734824E-03 0.2601700 at 30iterations 2.2147993E-04 3.8330078E-02 at 40iterations 5.1408246E-05 1.0082245E-02 at 50iterations finished qdiffx linear iterations at : 19:35:16 total time elapsed so far: 5.520000 # loops : 50 mean,max change (kT/e) : 5.1408246E-05 1.0082245E-02 energy calculations done at 5.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.680000 DelPhi exited at 19:35:17 5.688u 0.417s 0:06.53 93.2% 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 19:35:17 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 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: 1.916795 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): -12.10600 40.68000 ymin,ymax (A): -28.45500 23.72300 zmin,zma (A): -9.321000 46.39700 x,y,z range (A): 52.78600 52.17800 55.71800 scale (grids/A): 1.916795 object centre (A): 14.28700 -2.366000 18.53800 number of atom coordinates read : 2734 total number of charged atoms : 2597 net assigned charge : -1.999976 assigned positive charge : 409.9195 centred at (gu) : 89.98164 87.95660 91.74528 assigned negative charge : -411.9207 centred at (gu) : 90.04717 87.84731 92.06767 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81027 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25969 grid for indexing accessible points = 1.400000 m= 28996 mr = 54079 m= 5021 mr = 20741 m= 338 mr = 2934 m= 4 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 707 time to turn everything in is 0.6900000 number of dielectric boundary points 37521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 20484 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) : 0.6389318 object centre at (A) : 14.28700 -2.366000 18.53800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1547643E-02 -5.4549083E-02 midg,1,midg; midg,igrid,midg 2.2763615E-02 1.4248248E-02 1,midg,midg; igrid,midg,midg 1.9098489E-02 -2.1052329E-02 gauss-seidel spectral radius is 0.9986796 estimated iterations to convergence 218 setup time was (sec) 1.090000 now iterating at: 19:35:18 rms-change max change #iterations 4.474390 191.7183 at 10iterations 2.104024 72.20711 at 20iterations 1.000401 31.18353 at 30iterations 0.4703728 15.04248 at 40iterations 0.2231065 6.837439 at 50iterations 0.1057623 3.994137 at 60iterations 5.0101358E-02 1.829926 at 70iterations 2.3758912E-02 0.7396584 at 80iterations 1.1257614E-02 0.3723793 at 90iterations 5.3234170E-03 0.1664753 at 100iterations 2.5344905E-03 8.1027329E-02 at 110iterations 1.2053355E-03 3.8011074E-02 at 120iterations finished qdiffx linear iterations at : 19:35:31 total time elapsed so far: 13.27000 # loops : 120 mean,max change (kT/e) : 1.2053355E-03 3.8011074E-02 energy calculations done at 13.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.43000 DelPhi exited at 19:35:31 13.437u 0.491s 0:14.53 95.8% 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 Mon Oct 10 2011 at 19:35:31 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 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: 2.875193 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): -12.10600 40.68000 ymin,ymax (A): -28.45500 23.72300 zmin,zma (A): -9.321000 46.39700 x,y,z range (A): 52.78600 52.17800 55.71800 scale (grids/A): 2.875193 object centre (A): 14.28700 -2.366000 18.53800 number of atom coordinates read : 2734 total number of charged atoms : 2597 net assigned charge : -1.999976 assigned positive charge : 409.9195 centred at (gu) : 89.97232 86.93473 92.61784 assigned negative charge : -411.9207 centred at (gu) : 90.07063 86.77095 93.10136 start vw surface at 0.1200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 187092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25969 grid for indexing accessible points = 1.400000 m= 92098 mr = 131839 m= 34990 mr = 73442 m= 8926 mr = 27445 m= 1363 mr = 6498 m= 85 mr = 850 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 2417 time to turn everything in is 1.830000 number of dielectric boundary points 84448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 20774 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) : 1.916795 object centre at (A) : 14.28700 -2.366000 18.53800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3003646E-02 -0.6525038 midg,1,midg; midg,igrid,midg 0.3168965 0.1925389 1,midg,midg; igrid,midg,midg 0.3897621 -0.2520044 gauss-seidel spectral radius is 0.9992806 estimated iterations to convergence 294 setup time was (sec) 2.230000 now iterating at: 19:35:34 rms-change max change #iterations 10.55062 401.5984 at 10iterations 6.226069 133.7049 at 20iterations 3.651203 69.65324 at 30iterations 2.138448 43.90181 at 40iterations 1.249611 22.63521 at 50iterations 0.7288636 13.39913 at 60iterations 0.4244092 7.594782 at 70iterations 0.2473666 4.979919 at 80iterations 0.1436086 2.819664 at 90iterations 8.3359666E-02 1.552246 at 100iterations 4.8318125E-02 0.8951062 at 110iterations 2.8069377E-02 0.5153313 at 120iterations 1.6283959E-02 0.2887974 at 130iterations 9.4529921E-03 0.1602440 at 140iterations 5.4835682E-03 9.6982956E-02 at 150iterations 3.1863165E-03 5.6551188E-02 at 160iterations 1.8588449E-03 3.5270691E-02 at 170iterations 1.0903027E-03 1.9840240E-02 at 180iterations finished qdiffx linear iterations at : 19:35:56 total time elapsed so far: 23.64000 # loops : 180 mean,max change (kT/e) : 1.0903027E-03 1.9840240E-02 energy calculations done at 23.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.80000 DelPhi exited at 19:35:56 23.808u 0.499s 0:24.77 98.0% 0+0k 0+0io 0pf+0w