Tue Oct 11 08:32:53 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 Tue Oct 11 2011 at 08:32:53 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 = 2065 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7158513 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): 0.3050001 40.19200 ymin,ymax (A): -25.17300 18.15700 zmin,zma (A): -17.74400 31.98700 x,y,z range (A): 39.88700 43.33000 49.73100 scale (grids/A): 0.7158513 object centre (A): 20.24850 -3.508000 7.121500 number of atom coordinates read : 2065 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 88.75649 90.03149 91.29209 assigned negative charge : -305.3172 centred at (gu) : 88.68410 90.19180 91.31417 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6828 nv = 96 ne = 84 npr = 43234 no. pairs analyzed = 43234 no. exposed pairs = 2326 no. arc points = 16000 no. surface atoms = 793 nbur = 1272 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 428 mr = 3970 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 106 time to turn everything in is 0.1700000 number of dielectric boundary points 3220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1480 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7818 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.1147234E-08 8.2361773E-08 midg,1,midg; midg,igrid,midg 1.6829065E-07 -1.6998857E-08 1,midg,midg; igrid,midg,midg 4.3842899E-08 9.4464674E-08 gauss-seidel spectral radius is 0.9898167 estimated iterations to convergence 81 setup time was (sec) 0.3700000 now iterating at: 08:32:53 rms-change max change #iterations 0.2127953 31.37194 at 10iterations 2.6810681E-02 3.435321 at 20iterations 3.3744879E-03 0.4796553 at 30iterations 4.3031169E-04 5.7722092E-02 at 40iterations 5.3900556E-05 7.4672699E-03 at 50iterations finished qdiffx linear iterations at : 08:32:56 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 5.3900556E-05 7.4672699E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 08:32:57 3.319u 0.153s 0:03.78 91.5% 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 Tue Oct 11 2011 at 08:32:57 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 = 2065 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.147554 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): 0.3050001 40.19200 ymin,ymax (A): -25.17300 18.15700 zmin,zma (A): -17.74400 31.98700 x,y,z range (A): 39.88700 43.33000 49.73100 scale (grids/A): 2.147554 object centre (A): 20.24850 -3.508000 7.121500 number of atom coordinates read : 2065 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 86.26949 90.09438 93.87628 assigned negative charge : -305.3172 centred at (gu) : 86.05238 90.57547 93.94248 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73123 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16000 grid for indexing accessible points = 1.400000 m= 27622 mr = 52440 m= 5138 mr = 20735 m= 605 mr = 3408 m= 20 mr = 354 m= 0 mr = 4 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 3014 time to turn everything in is 0.3600000 number of dielectric boundary points 29567 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 15409 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) : 0.7158513 object centre at (A) : 20.24850 -3.508000 7.121500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4811891E-02 5.7838488E-02 midg,1,midg; midg,igrid,midg 5.3074073E-02 8.3378013E-03 1,midg,midg; igrid,midg,midg 2.9375317E-02 1.4765933E-02 gauss-seidel spectral radius is 0.9988444 estimated iterations to convergence 233 setup time was (sec) 0.5700000 now iterating at: 08:32:58 rms-change max change #iterations 4.635144 204.9759 at 10iterations 2.307832 78.26421 at 20iterations 1.145855 35.63376 at 30iterations 0.5715527 17.40700 at 40iterations 0.2856778 9.444966 at 50iterations 0.1418158 4.656344 at 60iterations 7.0830822E-02 2.312242 at 70iterations 3.5393372E-02 1.010695 at 80iterations 1.7565301E-02 0.5451241 at 90iterations 8.7749306E-03 0.2820816 at 100iterations 4.3838276E-03 0.1371613 at 110iterations 2.1896267E-03 6.7458153E-02 at 120iterations finished qdiffx linear iterations at : 08:33:04 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 2.1896267E-03 6.7458153E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 08:33:05 7.625u 0.195s 0:08.42 92.7% 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 Tue Oct 11 2011 at 08:33:05 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 = 2065 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.221331 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): 0.3050001 40.19200 ymin,ymax (A): -25.17300 18.15700 zmin,zma (A): -17.74400 31.98700 x,y,z range (A): 39.88700 43.33000 49.73100 scale (grids/A): 3.221331 object centre (A): 20.24850 -3.508000 7.121500 number of atom coordinates read : 2065 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 84.40430 90.14165 95.81450 assigned negative charge : -305.3172 centred at (gu) : 84.07860 90.86328 95.91390 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 168929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16000 grid for indexing accessible points = 1.400000 m= 87802 mr = 126118 m= 33812 mr = 73054 m= 9698 mr = 27659 m= 2208 mr = 7468 m= 319 mr = 1665 m= 20 mr = 239 m= 0 mr = 3 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 10223 time to turn everything in is 1.100000 number of dielectric boundary points 66582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 15496 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) : 2.147554 object centre at (A) : 20.24850 -3.508000 7.121500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3844510 0.4604102 midg,1,midg; midg,igrid,midg 0.3866394 8.7515220E-02 1,midg,midg; igrid,midg,midg 0.3352291 7.9782687E-02 gauss-seidel spectral radius is 0.9992945 estimated iterations to convergence 297 setup time was (sec) 1.330000 now iterating at: 08:33:07 rms-change max change #iterations 10.26750 388.3759 at 10iterations 6.076008 156.3363 at 20iterations 3.584678 85.86566 at 30iterations 2.116621 43.16201 at 40iterations 1.243322 23.98144 at 50iterations 0.7320150 14.25531 at 60iterations 0.4282719 7.772366 at 70iterations 0.2503900 4.429276 at 80iterations 0.1469545 2.877447 at 90iterations 8.6054154E-02 1.694991 at 100iterations 5.0402198E-02 0.9097805 at 110iterations 2.9489409E-02 0.5755920 at 120iterations 1.7337631E-02 0.3107796 at 130iterations 1.0207783E-02 0.1784716 at 140iterations 6.0348473E-03 0.1019202 at 150iterations 3.6126061E-03 6.7491531E-02 at 160iterations 2.1948167E-03 4.1839600E-02 at 170iterations 1.3707042E-03 2.5175095E-02 at 180iterations finished qdiffx linear iterations at : 08:33:18 total time elapsed so far: 12.39000 # loops : 180 mean,max change (kT/e) : 1.3707042E-03 2.5175095E-02 energy calculations done at 12.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 08:33:19 12.554u 0.208s 0:13.43 94.9% 0+0k 0+0io 0pf+0w