Mon Oct 10 16:58:57 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 16:58:57 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 = 2863 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: 0.5778471 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): -10.83500 39.88600 ymin,ymax (A): -23.66400 28.02000 zmin,zma (A): 13.78500 75.39300 x,y,z range (A): 50.72100 51.68400 61.60800 scale (grids/A): 0.5778471 object centre (A): 14.52550 2.178000 44.58900 number of atom coordinates read : 2863 total number of charged atoms : 2723 net assigned charge : 2.8878450E-05 assigned positive charge : 425.7114 centred at (gu) : 89.57469 89.55919 89.72346 assigned negative charge : -425.7124 centred at (gu) : 89.56425 89.70971 89.82577 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6344 nv = 96 ne = 84 npr = 57647 no. pairs analyzed = 57647 no. exposed pairs = 3521 no. arc points = 25334 no. surface atoms = 1189 nbur = 1674 mkacc time = 9.0000004E-02 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 = 1.484000 m= 262 mr = 3348 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3235 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2664 ## 309 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8120 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1031177E-09 -1.9192281E-09 midg,1,midg; midg,igrid,midg 3.2086405E-09 -2.7238005E-09 1,midg,midg; igrid,midg,midg -2.4562652E-10 1.7022724E-10 gauss-seidel spectral radius is 0.9845371 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 16:58:58 rms-change max change #iterations 9.6276090E-02 15.40670 at 10iterations 7.2553931E-03 1.161972 at 20iterations 5.6548102E-04 8.9202881E-02 at 30iterations 4.3996977E-05 8.5887909E-03 at 40iterations 3.6924284E-06 5.6338310E-04 at 50iterations finished qdiffx linear iterations at : 16:59:01 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 3.6924284E-06 5.6338310E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 16:59:01 3.376u 0.176s 0:03.98 88.9% 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 16:59:01 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 = 2863 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: 1.733541 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): -10.83500 39.88600 ymin,ymax (A): -23.66400 28.02000 zmin,zma (A): 13.78500 75.39300 x,y,z range (A): 50.72100 51.68400 61.60800 scale (grids/A): 1.733541 object centre (A): 14.52550 2.178000 44.58900 number of atom coordinates read : 2863 total number of charged atoms : 2723 net assigned charge : 2.8878450E-05 assigned positive charge : 425.7114 centred at (gu) : 88.72333 88.67689 89.16949 assigned negative charge : -425.7124 centred at (gu) : 88.69238 89.12891 89.47688 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25334 grid for indexing accessible points = 1.400000 m= 22580 mr = 47591 m= 2615 mr = 16136 m= 93 mr = 1454 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2734 time to turn everything in is 0.3400000 number of dielectric boundary points 29847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 255 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 21131 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) : 0.5778471 object centre at (A) : 14.52550 2.178000 44.58900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1341083E-03 -6.9049429E-03 midg,1,midg; midg,igrid,midg 6.8912893E-03 -1.9487774E-02 1,midg,midg; igrid,midg,midg -2.9500178E-03 -1.0916580E-02 gauss-seidel spectral radius is 0.9983873 estimated iterations to convergence 198 setup time was (sec) 0.5600000 now iterating at: 16:59:02 rms-change max change #iterations 3.699225 188.3487 at 10iterations 1.606427 57.58063 at 20iterations 0.7051969 24.32469 at 30iterations 0.3093525 11.99575 at 40iterations 0.1356494 4.731514 at 50iterations 5.9346437E-02 2.167244 at 60iterations 2.6012870E-02 0.9467981 at 70iterations 1.1388313E-02 0.3965225 at 80iterations 4.9879178E-03 0.1872702 at 90iterations 2.1955343E-03 8.8566780E-02 at 100iterations 9.6067839E-04 3.4015656E-02 at 110iterations 4.2107014E-04 1.3745308E-02 at 120iterations finished qdiffx linear iterations at : 16:59:09 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 4.2107014E-04 1.3745308E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 16:59:10 7.790u 0.190s 0:08.37 95.3% 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 16:59:10 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 = 2863 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: 2.600312 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): -10.83500 39.88600 ymin,ymax (A): -23.66400 28.02000 zmin,zma (A): 13.78500 75.39300 x,y,z range (A): 50.72100 51.68400 61.60800 scale (grids/A): 2.600312 object centre (A): 14.52550 2.178000 44.58900 number of atom coordinates read : 2863 total number of charged atoms : 2723 net assigned charge : 2.8878450E-05 assigned positive charge : 425.7114 centred at (gu) : 88.08484 88.01522 88.75393 assigned negative charge : -425.7124 centred at (gu) : 88.03847 88.69331 89.21531 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 161920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25334 grid for indexing accessible points = 1.400000 m= 76640 mr = 116108 m= 23526 mr = 61754 m= 4331 mr = 18316 m= 342 mr = 3114 m= 6 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 8791 time to turn everything in is 0.8500000 number of dielectric boundary points 67323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 21772 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) : 1.733541 object centre at (A) : 14.52550 2.178000 44.58900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9478648E-03 -6.8365097E-02 midg,1,midg; midg,igrid,midg 4.2535562E-02 -0.2296064 1,midg,midg; igrid,midg,midg -6.7068562E-02 -0.2100909 gauss-seidel spectral radius is 0.9991980 estimated iterations to convergence 279 setup time was (sec) 1.090000 now iterating at: 16:59:11 rms-change max change #iterations 9.127200 349.7665 at 10iterations 5.193608 144.1208 at 20iterations 2.938761 68.03284 at 30iterations 1.659597 39.92860 at 40iterations 0.9317312 24.36451 at 50iterations 0.5250224 11.61706 at 60iterations 0.2953861 7.239218 at 70iterations 0.1656385 3.238813 at 80iterations 9.3193516E-02 1.921381 at 90iterations 5.2318148E-02 1.031298 at 100iterations 2.9296573E-02 0.5536499 at 110iterations 1.6486308E-02 0.3834476 at 120iterations 9.2387339E-03 0.1850815 at 130iterations 5.1698270E-03 0.1003265 at 140iterations 2.9026822E-03 5.9646606E-02 at 150iterations 1.6287296E-03 3.2830238E-02 at 160iterations 9.1146363E-04 2.0215988E-02 at 170iterations 5.1208772E-04 9.4674826E-03 at 180iterations finished qdiffx linear iterations at : 16:59:22 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 5.1208772E-04 9.4674826E-03 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 16:59:23 12.303u 0.215s 0:13.62 91.8% 0+0k 0+0io 0pf+0w