Mon Oct 10 14:10:46 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+sph2.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 = amb2.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 14:10:46 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4320 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5849395 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): -25.70200 35.15900 ymin,ymax (A): 38.08600 98.66600 zmin,zma (A): 31.02100 90.57800 x,y,z range (A): 60.86100 60.58000 59.55699 scale (grids/A): 0.5849395 object centre (A): 4.728498 68.37600 60.79950 number of atom coordinates read : 4320 total number of charged atoms : 4161 net assigned charge : -1.985960 assigned positive charge : 650.2196 centred at (gu) : 90.70736 87.79811 88.71942 assigned negative charge : -652.2086 centred at (gu) : 90.59083 87.93064 88.86926 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 9674 nv = 96 ne = 84 npr = 89549 no. pairs analyzed = 89549 no. exposed pairs = 4931 no. arc points = 33635 no. surface atoms = 1677 nbur = 2643 mkacc time = 0.1500000 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= 460 mr = 5667 m= 4 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 85 time to turn everything in is 0.3000000 number of dielectric boundary points 4419 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3559 ## 402 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 12548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5435981E-09 -4.8133617E-09 midg,1,midg; midg,igrid,midg 7.1144335E-09 -3.4874246E-09 1,midg,midg; igrid,midg,midg -4.4035131E-09 4.2605426E-09 gauss-seidel spectral radius is 0.9850126 estimated iterations to convergence 67 setup time was (sec) 0.4800000 now iterating at: 14:10:47 rms-change max change #iterations 0.1299434 18.93434 at 10iterations 1.0757003E-02 1.600218 at 20iterations 1.3234629E-03 0.1588135 at 30iterations 3.4974123E-04 3.7048340E-02 at 40iterations 1.2774036E-04 1.4658928E-02 at 50iterations finished qdiffx linear iterations at : 14:10:50 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.2774036E-04 1.4658928E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 14:10:50 3.505u 0.192s 0:04.24 87.0% 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 14:10:50 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4320 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.754818 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): -25.70200 35.15900 ymin,ymax (A): 38.08600 98.66600 zmin,zma (A): 31.02100 90.57800 x,y,z range (A): 60.86100 60.58000 59.55699 scale (grids/A): 1.754818 object centre (A): 4.728498 68.37600 60.79950 number of atom coordinates read : 4320 total number of charged atoms : 4161 net assigned charge : -1.985960 assigned positive charge : 650.2196 centred at (gu) : 92.12091 83.39322 86.15701 assigned negative charge : -652.2086 centred at (gu) : 91.77190 83.79150 86.60728 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 107402 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33635 grid for indexing accessible points = 1.400000 m= 37971 mr = 78154 m= 5133 mr = 28409 m= 197 mr = 3136 m= 0 mr = 55 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 5516 time to turn everything in is 0.5000000 number of dielectric boundary points 40949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 335 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 32374 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) : 0.5849395 object centre at (A) : 4.728498 68.37600 60.79950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8344882E-02 -3.1835850E-02 midg,1,midg; midg,igrid,midg 4.3830082E-02 -8.2300911E-03 1,midg,midg; igrid,midg,midg -1.8085662E-02 3.9393470E-02 gauss-seidel spectral radius is 0.9985487 estimated iterations to convergence 208 setup time was (sec) 0.7300000 now iterating at: 14:10:51 rms-change max change #iterations 4.866947 158.9215 at 10iterations 2.218185 67.04309 at 20iterations 1.013369 28.50130 at 30iterations 0.4650845 12.92608 at 40iterations 0.2143991 6.169937 at 50iterations 9.7687423E-02 2.653666 at 60iterations 4.5011178E-02 1.365954 at 70iterations 2.0675497E-02 0.6144323 at 80iterations 9.5393853E-03 0.2504463 at 90iterations 4.4378536E-03 0.1324081 at 100iterations 2.1100203E-03 5.6079865E-02 at 110iterations 1.0379098E-03 2.9935837E-02 at 120iterations finished qdiffx linear iterations at : 14:10:58 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.0379098E-03 2.9935837E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 14:10:59 8.026u 0.206s 0:08.59 95.6% 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 Mon Oct 10 2011 at 14:10:59 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4320 !!! WARNING: HIT 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.632228 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): -25.70200 35.15900 ymin,ymax (A): 38.08600 98.66600 zmin,zma (A): 31.02100 90.57800 x,y,z range (A): 60.86100 60.58000 59.55699 scale (grids/A): 2.632228 object centre (A): 4.728498 68.37600 60.79950 number of atom coordinates read : 4320 total number of charged atoms : 4161 net assigned charge : -1.985960 assigned positive charge : 650.2196 centred at (gu) : 93.18121 80.08956 84.23527 assigned negative charge : -652.2086 centred at (gu) : 92.65788 80.68700 84.91102 start vw surface at 0.1200000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 249033 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33635 grid for indexing accessible points = 1.400000 m= 127107 mr = 189182 m= 41930 mr = 105431 m= 9018 mr = 33764 m= 1026 mr = 6840 m= 26 mr = 610 m= 0 mr = 4 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 18599 time to turn everything in is 1.310000 number of dielectric boundary points 92309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 33280 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) : 1.754818 object centre at (A) : 4.728498 68.37600 60.79950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9906104 -0.3592321 midg,1,midg; midg,igrid,midg 0.5797167 -9.3040437E-02 1,midg,midg; igrid,midg,midg -0.3309189 0.5453253 gauss-seidel spectral radius is 0.9992626 estimated iterations to convergence 291 setup time was (sec) 1.550000 now iterating at: 14:11:01 rms-change max change #iterations 11.79078 338.0376 at 10iterations 6.918575 134.3304 at 20iterations 4.032657 71.26668 at 30iterations 2.340359 41.33913 at 40iterations 1.361231 22.33381 at 50iterations 0.7875484 14.20778 at 60iterations 0.4546013 7.204513 at 70iterations 0.2631161 4.105860 at 80iterations 0.1519969 2.420090 at 90iterations 8.7797038E-02 1.438385 at 100iterations 5.0691951E-02 0.8231564 at 110iterations 2.9315038E-02 0.5406151 at 120iterations 1.6963203E-02 0.2662015 at 130iterations 9.8883240E-03 0.1487427 at 140iterations 5.8140331E-03 9.2405319E-02 at 150iterations 3.4898866E-03 5.5212975E-02 at 160iterations 2.1541240E-03 3.5468102E-02 at 170iterations 1.3841684E-03 2.1590233E-02 at 180iterations finished qdiffx linear iterations at : 14:11:12 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 1.3841684E-03 2.1590233E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.30000 DelPhi exited at 14:11:13 13.299u 0.222s 0:13.97 96.7% 0+0k 0+0io 0pf+0w