Sat Oct 8 17:02:29 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 17:02:29 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 = 4906 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4870841 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): -3.937000 62.74400 ymin,ymax (A): -30.27000 30.87400 zmin,zma (A): -23.79400 49.29400 x,y,z range (A): 66.68100 61.14400 73.08800 scale (grids/A): 0.4870841 object centre (A): 29.40350 0.3020000 12.75000 number of atom coordinates read : 4906 total number of charged atoms : 4750 net assigned charge : -12.99998 assigned positive charge : 742.8566 centred at (gu) : 90.95268 91.23260 90.03384 assigned negative charge : -755.8618 centred at (gu) : 90.96353 91.18142 90.05235 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 7539 nv = 96 ne = 84 npr = 94782 no. pairs analyzed = 94782 no. exposed pairs = 6668 no. arc points = 47394 no. surface atoms = 2198 nbur = 2708 mkacc time = 0.2000000 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 = 1.764000 m= 259 mr = 3640 m= 0 mr = 6 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 4152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4474 ## 812 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 10182 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3861633E-11 -8.0350428E-11 midg,1,midg; midg,igrid,midg -7.9558360E-11 -1.7655438E-11 1,midg,midg; igrid,midg,midg -4.0079610E-11 -9.3560035E-11 gauss-seidel spectral radius is 0.9784808 estimated iterations to convergence 56 setup time was (sec) 0.7200000 now iterating at: 17:02:30 rms-change max change #iterations 5.1795732E-02 9.794350 at 10iterations 2.7162745E-03 0.4340363 at 20iterations 3.4655692E-04 7.3886871E-02 at 30iterations 9.3823153E-05 2.1182060E-02 at 40iterations 2.7096727E-05 6.1349869E-03 at 50iterations finished qdiffx linear iterations at : 17:02:33 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.7096727E-05 6.1349869E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 17:02:33 3.494u 0.181s 0:03.96 92.6% 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 Sat Oct 8 2011 at 17:02:33 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 = 4906 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.461252 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): -3.937000 62.74400 ymin,ymax (A): -30.27000 30.87400 zmin,zma (A): -23.79400 49.29400 x,y,z range (A): 66.68100 61.14400 73.08800 scale (grids/A): 1.461252 object centre (A): 29.40350 0.3020000 12.75000 number of atom coordinates read : 4906 total number of charged atoms : 4750 net assigned charge : -12.99998 assigned positive charge : 742.8566 centred at (gu) : 92.85669 93.69612 90.10023 assigned negative charge : -755.8618 centred at (gu) : 92.89045 93.54417 90.15698 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 85080 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47394 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 23281 mr = 55755 m= 1714 mr = 14760 m= 30 mr = 659 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 583 time to turn everything in is 0.6100000 number of dielectric boundary points 38931 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 731 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 35034 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) : 0.4870841 object centre at (A) : 29.40350 0.3020000 12.75000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5975003E-03 -2.8244581E-02 midg,1,midg; midg,igrid,midg -9.3773473E-03 -5.5800453E-03 1,midg,midg; igrid,midg,midg 2.0706484E-03 -3.6100962E-03 gauss-seidel spectral radius is 0.9979176 estimated iterations to convergence 174 setup time was (sec) 0.9000000 now iterating at: 17:02:34 rms-change max change #iterations 3.458356 136.2219 at 10iterations 1.349851 46.98707 at 20iterations 0.5288204 19.80623 at 30iterations 0.2071264 7.524792 at 40iterations 8.1100821E-02 2.804178 at 50iterations 3.1874526E-02 1.247090 at 60iterations 1.2532827E-02 0.4410419 at 70iterations 4.9552177E-03 0.1801147 at 80iterations 1.9694949E-03 6.4680099E-02 at 90iterations 7.9911092E-04 2.7875900E-02 at 100iterations 3.3877249E-04 1.3854027E-02 at 110iterations 1.5411900E-04 6.2408447E-03 at 120iterations finished qdiffx linear iterations at : 17:02:41 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 1.5411900E-04 6.2408447E-03 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 17:02:41 7.646u 0.228s 0:08.19 95.9% 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 Sat Oct 8 2011 at 17:02:41 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 = 4906 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.191878 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): -3.937000 62.74400 ymin,ymax (A): -30.27000 30.87400 zmin,zma (A): -23.79400 49.29400 x,y,z range (A): 66.68100 61.14400 73.08800 scale (grids/A): 2.191878 object centre (A): 29.40350 0.3020000 12.75000 number of atom coordinates read : 4906 total number of charged atoms : 4750 net assigned charge : -12.99998 assigned positive charge : 742.8566 centred at (gu) : 94.28445 95.54395 90.15000 assigned negative charge : -755.8618 centred at (gu) : 94.33575 95.31612 90.23544 start vw surface at 0.2000000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 198212 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47394 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 85094 mr = 137924 m= 19491 mr = 64417 m= 2338 mr = 13613 m= 84 mr = 1358 m= 0 mr = 16 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 2001 time to turn everything in is 1.440000 number of dielectric boundary points 87891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 37847 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) : 1.461252 object centre at (A) : 29.40350 0.3020000 12.75000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2378594 -0.4865135 midg,1,midg; midg,igrid,midg -0.2753002 -9.3735948E-02 1,midg,midg; igrid,midg,midg 2.7858661E-02 -0.1050098 gauss-seidel spectral radius is 0.9990969 estimated iterations to convergence 263 setup time was (sec) 1.740000 now iterating at: 17:02:43 rms-change max change #iterations 9.740403 267.6878 at 10iterations 5.489465 151.0137 at 20iterations 3.066593 81.48514 at 30iterations 1.702905 38.25076 at 40iterations 0.9393998 20.08679 at 50iterations 0.5170978 10.75729 at 60iterations 0.2836300 5.888775 at 70iterations 0.1550519 3.284774 at 80iterations 8.4868163E-02 1.614399 at 90iterations 4.6286028E-02 1.068837 at 100iterations 2.5225509E-02 0.4747028 at 110iterations 1.3758342E-02 0.2711535 at 120iterations 7.4907281E-03 0.1583252 at 130iterations 4.0751318E-03 7.6948166E-02 at 140iterations 2.2236609E-03 4.8210144E-02 at 150iterations 1.2154968E-03 2.3865730E-02 at 160iterations 6.6804723E-04 1.2367249E-02 at 170iterations 3.6930610E-04 7.6482296E-03 at 180iterations finished qdiffx linear iterations at : 17:02:54 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 3.6930610E-04 7.6482296E-03 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 17:02:54 12.556u 0.254s 0:13.09 97.7% 0+0k 0+0io 0pf+0w