Mon Oct 10 14:00:54 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 14:00:54 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6410719 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): -3.832000 34.68500 ymin,ymax (A): -4.350000 49.20000 zmin,zma (A): -24.12200 31.41000 x,y,z range (A): 38.51700 53.55000 55.53200 scale (grids/A): 0.6410719 object centre (A): 15.42650 22.42500 3.644000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 291.0260 centred at (gu) : 90.38763 92.56767 90.09738 assigned negative charge : -286.0263 centred at (gu) : 90.42816 92.61613 90.04746 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5598 nv = 96 ne = 84 npr = 39955 no. pairs analyzed = 39955 no. exposed pairs = 2491 no. arc points = 17449 no. surface atoms = 851 nbur = 1111 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 282 mr = 3120 m= 0 mr = 21 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1737 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6517 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1220146E-09 1.2195495E-08 midg,1,midg; midg,igrid,midg 6.9437056E-09 5.4378675E-09 1,midg,midg; igrid,midg,midg 1.0263737E-08 4.3296642E-09 gauss-seidel spectral radius is 0.9873379 estimated iterations to convergence 73 setup time was (sec) 0.5000000 now iterating at: 14:00:54 rms-change max change #iterations 0.1262622 22.12376 at 10iterations 1.2598935E-02 2.318413 at 20iterations 1.2358628E-03 0.2132072 at 30iterations 1.2367601E-04 2.2491455E-02 at 40iterations 1.2223487E-05 1.9416809E-03 at 50iterations finished qdiffx linear iterations at : 14:00:57 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.2223487E-05 1.9416809E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:00:59 3.358u 0.141s 0:05.10 68.4% 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 14:00:59 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.923216 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): -3.832000 34.68500 ymin,ymax (A): -4.350000 49.20000 zmin,zma (A): -24.12200 31.41000 x,y,z range (A): 38.51700 53.55000 55.53200 scale (grids/A): 1.923216 object centre (A): 15.42650 22.42500 3.644000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 291.0260 centred at (gu) : 91.16261 97.70303 90.29209 assigned negative charge : -286.0263 centred at (gu) : 91.28453 97.84857 90.14266 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 59737 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17449 grid for indexing accessible points = 1.400000 m= 22371 mr = 41260 m= 3235 mr = 17087 m= 142 mr = 2008 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 834 time to turn everything in is 0.4700000 number of dielectric boundary points 25101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 14434 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) : 0.6410719 object centre at (A) : 15.42650 22.42500 3.644000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7296941E-02 2.1123398E-02 midg,1,midg; midg,igrid,midg 2.9032534E-02 1.0591719E-02 1,midg,midg; igrid,midg,midg 3.9345268E-03 7.0818997E-04 gauss-seidel spectral radius is 0.9985828 estimated iterations to convergence 211 setup time was (sec) 0.7600000 now iterating at: 14:01:00 rms-change max change #iterations 3.640312 171.5103 at 10iterations 1.676837 62.57709 at 20iterations 0.7760199 27.56966 at 30iterations 0.3582560 12.14273 at 40iterations 0.1655662 6.246655 at 50iterations 7.6421790E-02 3.116715 at 60iterations 3.5060018E-02 1.172555 at 70iterations 1.6193382E-02 0.5341709 at 80iterations 7.4709621E-03 0.2580572 at 90iterations 3.4571243E-03 0.1196747 at 100iterations 1.5930171E-03 6.1014414E-02 at 110iterations 7.3530251E-04 2.5274277E-02 at 120iterations finished qdiffx linear iterations at : 14:01:07 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 7.3530251E-04 2.5274277E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 14:01:07 7.862u 0.181s 0:08.52 94.3% 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 14:01:07 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.884823 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): -3.832000 34.68500 ymin,ymax (A): -4.350000 49.20000 zmin,zma (A): -24.12200 31.41000 x,y,z range (A): 38.51700 53.55000 55.53200 scale (grids/A): 2.884823 object centre (A): 15.42650 22.42500 3.644000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 291.0260 centred at (gu) : 91.74393 101.5546 90.43813 assigned negative charge : -286.0263 centred at (gu) : 91.92693 101.7728 90.21413 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 137928 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17449 grid for indexing accessible points = 1.400000 m= 71659 mr = 99696 m= 26590 mr = 59603 m= 5686 mr = 22002 m= 605 mr = 4249 m= 25 mr = 337 m= 0 mr = 7 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 3142 time to turn everything in is 1.140000 number of dielectric boundary points 56599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 14640 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) : 1.923216 object centre at (A) : 15.42650 22.42500 3.644000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.063013 9.5727675E-02 midg,1,midg; midg,igrid,midg 0.2812783 9.8370202E-03 1,midg,midg; igrid,midg,midg 1.4779395E-02 1.0413382E-02 gauss-seidel spectral radius is 0.9992307 estimated iterations to convergence 285 setup time was (sec) 1.430000 now iterating at: 14:01:09 rms-change max change #iterations 8.662962 350.6430 at 10iterations 5.015425 151.4447 at 20iterations 2.875351 73.52956 at 30iterations 1.645045 53.11559 at 40iterations 0.9409589 18.49644 at 50iterations 0.5347916 11.91394 at 60iterations 0.3048373 6.339264 at 70iterations 0.1734715 3.760193 at 80iterations 9.8408960E-02 1.955822 at 90iterations 5.6095496E-02 1.215775 at 100iterations 3.1877659E-02 0.6262183 at 110iterations 1.8072248E-02 0.3594589 at 120iterations 1.0252372E-02 0.1957569 at 130iterations 5.8233617E-03 0.1116505 at 140iterations 3.3070946E-03 6.7169189E-02 at 150iterations 1.8766556E-03 3.5653144E-02 at 160iterations 1.0669243E-03 2.1321297E-02 at 170iterations 6.0535374E-04 1.3866425E-02 at 180iterations finished qdiffx linear iterations at : 14:01:19 total time elapsed so far: 11.31000 # loops : 180 mean,max change (kT/e) : 6.0535374E-04 1.3866425E-02 energy calculations done at 11.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.50000 DelPhi exited at 14:01:20 11.499u 0.184s 0:12.70 91.8% 0+0k 0+0io 0pf+0w