Mon Oct 10 17:02:05 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 17:02:05 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 = 2914 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5881090 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): -26.84100 33.69200 ymin,ymax (A): -10.87200 38.74600 zmin,zma (A): 4.908000 61.31300 x,y,z range (A): 60.53300 49.61800 56.40500 scale (grids/A): 0.5881090 object centre (A): 3.425499 13.93700 33.11050 number of atom coordinates read : 2914 total number of charged atoms : 2773 net assigned charge : -3.999967 assigned positive charge : 436.5060 centred at (gu) : 90.31617 90.93317 91.54263 assigned negative charge : -440.5072 centred at (gu) : 90.37047 90.83173 91.60873 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6598 nv = 96 ne = 84 npr = 58370 no. pairs analyzed = 58370 no. exposed pairs = 3852 no. arc points = 27084 no. surface atoms = 1292 nbur = 1622 mkacc time = 0.1000000 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 = 1.456000 m= 300 mr = 3351 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2100000 number of dielectric boundary points 3540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2716 ## 284 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8382 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8717519E-10 -4.3401638E-09 midg,1,midg; midg,igrid,midg -3.2646792E-09 2.1364130E-09 1,midg,midg; igrid,midg,midg 3.5689102E-10 -2.8925817E-09 gauss-seidel spectral radius is 0.9850715 estimated iterations to convergence 67 setup time was (sec) 0.3900000 now iterating at: 17:02:06 rms-change max change #iterations 0.1042155 16.96681 at 10iterations 8.2197860E-03 1.329369 at 20iterations 6.5959757E-04 9.2877388E-02 at 30iterations 5.6358695E-05 7.9555511E-03 at 40iterations 5.7945840E-06 1.0690689E-03 at 50iterations finished qdiffx linear iterations at : 17:02:09 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 5.7945840E-06 1.0690689E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 17:02:09 3.338u 0.166s 0:04.22 82.7% 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 17:02:09 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 = 2914 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: 1.764327 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): -26.84100 33.69200 ymin,ymax (A): -10.87200 38.74600 zmin,zma (A): 4.908000 61.31300 x,y,z range (A): 60.53300 49.61800 56.40500 scale (grids/A): 1.764327 object centre (A): 3.425499 13.93700 33.11050 number of atom coordinates read : 2914 total number of charged atoms : 2773 net assigned charge : -3.999967 assigned positive charge : 436.5060 centred at (gu) : 90.94778 92.79872 94.62690 assigned negative charge : -440.5072 centred at (gu) : 91.11113 92.49489 94.82570 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27084 grid for indexing accessible points = 1.400000 m= 23060 mr = 48089 m= 2722 mr = 15663 m= 129 mr = 1326 m= 0 mr = 12 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 238 time to turn everything in is 0.3500000 number of dielectric boundary points 32855 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 21617 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) : 0.5881090 object centre at (A) : 3.425499 13.93700 33.11050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3255475E-02 -3.4617248E-04 midg,1,midg; midg,igrid,midg -1.7271284E-02 4.2965310E-04 1,midg,midg; igrid,midg,midg 1.3060791E-02 -3.7865493E-02 gauss-seidel spectral radius is 0.9984477 estimated iterations to convergence 201 setup time was (sec) 0.5600000 now iterating at: 17:02:10 rms-change max change #iterations 3.883135 176.5304 at 10iterations 1.710075 60.44067 at 20iterations 0.7623366 28.52847 at 30iterations 0.3372415 11.07620 at 40iterations 0.1501851 4.796025 at 50iterations 6.6883974E-02 2.344307 at 60iterations 2.9738575E-02 0.9766693 at 70iterations 1.3249321E-02 0.4464731 at 80iterations 5.8824075E-03 0.1991730 at 90iterations 2.6160269E-03 8.8216782E-02 at 100iterations 1.1688535E-03 3.9960861E-02 at 110iterations 5.2079000E-04 1.7990112E-02 at 120iterations finished qdiffx linear iterations at : 17:02:17 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 5.2079000E-04 1.7990112E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 17:02:18 7.608u 0.188s 0:08.45 92.0% 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 17:02:18 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 = 2914 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: 2.646491 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): -26.84100 33.69200 ymin,ymax (A): -10.87200 38.74600 zmin,zma (A): 4.908000 61.31300 x,y,z range (A): 60.53300 49.61800 56.40500 scale (grids/A): 2.646491 object centre (A): 3.425499 13.93700 33.11050 number of atom coordinates read : 2914 total number of charged atoms : 2773 net assigned charge : -3.999967 assigned positive charge : 436.5060 centred at (gu) : 91.42164 94.19792 96.94028 assigned negative charge : -440.5072 centred at (gu) : 91.66660 93.74220 97.23849 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 167069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27084 grid for indexing accessible points = 1.400000 m= 77618 mr = 117596 m= 23969 mr = 60868 m= 4358 mr = 17994 m= 417 mr = 2659 m= 19 mr = 181 m= 2 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 819 time to turn everything in is 0.8900000 number of dielectric boundary points 74154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 22181 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) : 1.764327 object centre at (A) : 3.425499 13.93700 33.11050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1822549 0.1327740 midg,1,midg; midg,igrid,midg -0.2171558 -1.1175089E-02 1,midg,midg; igrid,midg,midg 0.1872429 -0.4449493 gauss-seidel spectral radius is 0.9992206 estimated iterations to convergence 283 setup time was (sec) 1.110000 now iterating at: 17:02:19 rms-change max change #iterations 9.715205 451.8878 at 10iterations 5.688503 176.7361 at 20iterations 3.284142 77.65048 at 30iterations 1.889859 41.67733 at 40iterations 1.084221 23.65082 at 50iterations 0.6196089 13.54154 at 60iterations 0.3526843 7.514532 at 70iterations 0.2011174 4.015232 at 80iterations 0.1141100 2.153171 at 90iterations 6.4765714E-02 1.246900 at 100iterations 3.6860339E-02 0.6924896 at 110iterations 2.0897217E-02 0.4094467 at 120iterations 1.1817846E-02 0.2371511 at 130iterations 6.7060934E-03 0.1374073 at 140iterations 3.7952655E-03 7.6530457E-02 at 150iterations 2.1508606E-03 4.2320251E-02 at 160iterations 1.2187239E-03 2.3981571E-02 at 170iterations 6.9058622E-04 1.2700021E-02 at 180iterations finished qdiffx linear iterations at : 17:02:30 total time elapsed so far: 12.12000 # loops : 180 mean,max change (kT/e) : 6.9058622E-04 1.2700021E-02 energy calculations done at 12.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.26000 DelPhi exited at 17:02:31 12.262u 0.185s 0:13.07 95.1% 0+0k 0+0io 0pf+0w