Sat Oct 8 23:07:14 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 23:07:14 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 = 2402 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: 0.6480386 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): -13.73000 41.20500 ymin,ymax (A): 12.53900 65.82600 zmin,zma (A): 2.367000 45.80600 x,y,z range (A): 54.93500 53.28700 43.43900 scale (grids/A): 0.6480386 object centre (A): 13.73750 39.18250 24.08650 number of atom coordinates read : 2402 total number of charged atoms : 2266 net assigned charge : 12.00002 assigned positive charge : 351.3993 centred at (gu) : 89.97132 88.90690 89.44844 assigned negative charge : -339.4000 centred at (gu) : 90.01862 88.91694 89.53525 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6769 nv = 96 ne = 84 npr = 48144 no. pairs analyzed = 48144 no. exposed pairs = 3120 no. arc points = 22521 no. surface atoms = 1048 nbur = 1354 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 423 mr = 3508 m= 4 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2163 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8091 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6710169E-08 9.6762500E-09 midg,1,midg; midg,igrid,midg 2.8943925E-08 1.6492216E-08 1,midg,midg; igrid,midg,midg 2.7958237E-08 1.5733034E-08 gauss-seidel spectral radius is 0.9876498 estimated iterations to convergence 74 setup time was (sec) 0.4000000 now iterating at: 23:07:14 rms-change max change #iterations 0.1430744 20.52105 at 10iterations 1.4663340E-02 2.245224 at 20iterations 1.6140726E-03 0.2378139 at 30iterations 2.7987873E-04 4.7929764E-02 at 40iterations 8.3539628E-05 1.6502380E-02 at 50iterations finished qdiffx linear iterations at : 23:07:17 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 8.3539628E-05 1.6502380E-02 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 23:07:18 3.606u 0.195s 0:04.09 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 23:07:18 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 = 2402 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: 1.944116 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): -13.73000 41.20500 ymin,ymax (A): 12.53900 65.82600 zmin,zma (A): 2.367000 45.80600 x,y,z range (A): 54.93500 53.28700 43.43900 scale (grids/A): 1.944116 object centre (A): 13.73750 39.18250 24.08650 number of atom coordinates read : 2402 total number of charged atoms : 2266 net assigned charge : 12.00002 assigned positive charge : 351.3993 centred at (gu) : 89.91355 86.72047 88.34484 assigned negative charge : -339.4000 centred at (gu) : 90.05589 86.75111 88.60566 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22521 grid for indexing accessible points = 1.400000 m= 26326 mr = 48729 m= 4750 mr = 18898 m= 356 mr = 2877 m= 10 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 33568 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17896 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) : 0.6480386 object centre at (A) : 13.73750 39.18250 24.08650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2397743E-02 2.3009148E-03 midg,1,midg; midg,igrid,midg 2.3661088E-02 5.5105753E-02 1,midg,midg; igrid,midg,midg 6.1329611E-02 3.0485535E-02 gauss-seidel spectral radius is 0.9986773 estimated iterations to convergence 218 setup time was (sec) 0.6100000 now iterating at: 23:07:19 rms-change max change #iterations 4.079865 169.7718 at 10iterations 1.926530 69.74019 at 20iterations 0.9117885 28.99249 at 30iterations 0.4310607 14.87955 at 40iterations 0.2037058 6.844875 at 50iterations 9.6612260E-02 2.942277 at 60iterations 4.5751277E-02 1.473219 at 70iterations 2.1750312E-02 0.7550316 at 80iterations 1.0294084E-02 0.3077812 at 90iterations 4.9318685E-03 0.1513729 at 100iterations 2.3923654E-03 7.4711800E-02 at 110iterations 1.1840598E-03 4.2497158E-02 at 120iterations finished qdiffx linear iterations at : 23:07:26 total time elapsed so far: 8.120000 # loops : 120 mean,max change (kT/e) : 1.1840598E-03 4.2497158E-02 energy calculations done at 8.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.260000 DelPhi exited at 23:07:27 8.259u 0.233s 0:08.82 96.1% 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 23:07:27 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 = 2402 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: 2.916174 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): -13.73000 41.20500 ymin,ymax (A): 12.53900 65.82600 zmin,zma (A): 2.367000 45.80600 x,y,z range (A): 54.93500 53.28700 43.43900 scale (grids/A): 2.916174 object centre (A): 13.73750 39.18250 24.08650 number of atom coordinates read : 2402 total number of charged atoms : 2266 net assigned charge : 12.00002 assigned positive charge : 351.3993 centred at (gu) : 89.87024 85.08061 87.51720 assigned negative charge : -339.4000 centred at (gu) : 90.08378 85.12652 87.90864 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 168232 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22521 grid for indexing accessible points = 1.400000 m= 83286 mr = 118886 m= 31840 mr = 66675 m= 8749 mr = 25146 m= 1471 mr = 6328 m= 127 mr = 936 m= 7 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 75712 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 18128 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) : 1.944116 object centre at (A) : 13.73750 39.18250 24.08650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2844380 -2.1402717E-03 midg,1,midg; midg,igrid,midg 0.2445613 0.6794059 1,midg,midg; igrid,midg,midg 0.6174625 0.4064411 gauss-seidel spectral radius is 0.9992744 estimated iterations to convergence 293 setup time was (sec) 1.220000 now iterating at: 23:07:28 rms-change max change #iterations 9.706370 467.4071 at 10iterations 5.734324 123.0696 at 20iterations 3.377353 74.23928 at 30iterations 1.973994 40.92187 at 40iterations 1.152801 25.31334 at 50iterations 0.6712961 13.41260 at 60iterations 0.3914042 8.213086 at 70iterations 0.2272262 4.343836 at 80iterations 0.1320122 2.548800 at 90iterations 7.6680586E-02 1.422404 at 100iterations 4.4494163E-02 0.8154879 at 110iterations 2.5793917E-02 0.4842148 at 120iterations 1.4954303E-02 0.2807255 at 130iterations 8.7008178E-03 0.1621552 at 140iterations 5.0614355E-03 9.1110229E-02 at 150iterations 2.9760874E-03 5.4434061E-02 at 160iterations 1.7719237E-03 3.5397530E-02 at 170iterations 1.0822082E-03 2.4778366E-02 at 180iterations finished qdiffx linear iterations at : 23:07:40 total time elapsed so far: 13.37000 # loops : 180 mean,max change (kT/e) : 1.0822082E-03 2.4778366E-02 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.52000 DelPhi exited at 23:07:41 13.520u 0.255s 0:14.04 98.0% 0+0k 0+0io 0pf+0w