Tue Oct 11 06:14:53 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+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 Tue Oct 11 2011 at 06:14:53 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2019 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: 0.7298971 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): 26.58600 72.12000 ymin,ymax (A): 44.26200 82.43400 zmin,zma (A): -60.83200 -12.05800 x,y,z range (A): 45.53400 38.17200 48.77399 scale (grids/A): 0.7298971 object centre (A): 49.35300 63.34800 -36.44500 number of atom coordinates read : 2019 total number of charged atoms : 1889 net assigned charge : 4.500006 assigned positive charge : 305.7132 centred at (gu) : 89.94238 89.32127 88.57744 assigned negative charge : -301.2132 centred at (gu) : 90.08657 89.43190 88.57100 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7450 nv = 96 ne = 84 npr = 40637 no. pairs analyzed = 40637 no. exposed pairs = 2575 no. arc points = 17353 no. surface atoms = 875 nbur = 1144 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 547 mr = 4251 m= 5 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1464 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 7909 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5114237E-08 5.2423719E-08 midg,1,midg; midg,igrid,midg 1.6797017E-07 -2.0320147E-08 1,midg,midg; igrid,midg,midg 1.7489880E-07 -4.9718704E-08 gauss-seidel spectral radius is 0.9902068 estimated iterations to convergence 82 setup time was (sec) 0.5100000 now iterating at: 06:14:54 rms-change max change #iterations 0.2322323 29.23275 at 10iterations 3.0814607E-02 4.023642 at 20iterations 4.3508592E-03 0.6162720 at 30iterations 8.5352955E-04 0.1115532 at 40iterations 2.6585456E-04 3.1875610E-02 at 50iterations finished qdiffx linear iterations at : 06:14:58 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 2.6585456E-04 3.1875610E-02 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.340000 DelPhi exited at 06:14:58 4.349u 0.394s 0:05.05 93.6% 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 Tue Oct 11 2011 at 06:14:58 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2019 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.189692 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): 26.58600 72.12000 ymin,ymax (A): 44.26200 82.43400 zmin,zma (A): -60.83200 -12.05800 x,y,z range (A): 45.53400 38.17200 48.77399 scale (grids/A): 2.189692 object centre (A): 49.35300 63.34800 -36.44500 number of atom coordinates read : 2019 total number of charged atoms : 1889 net assigned charge : 4.500006 assigned positive charge : 305.7132 centred at (gu) : 89.82726 87.96375 85.73238 assigned negative charge : -301.2132 centred at (gu) : 90.25978 88.29587 85.71301 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17353 grid for indexing accessible points = 1.400000 m= 33168 mr = 54969 m= 7110 mr = 25345 m= 740 mr = 4881 m= 16 mr = 357 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 33428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 15019 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) : 0.7298971 object centre at (A) : 49.35300 63.34800 -36.44500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1736261E-03 1.6962487E-02 midg,1,midg; midg,igrid,midg 4.3680720E-02 -6.8727448E-03 1,midg,midg; igrid,midg,midg 4.9782578E-02 2.9618651E-02 gauss-seidel spectral radius is 0.9988888 estimated iterations to convergence 237 setup time was (sec) 0.9600000 now iterating at: 06:14:59 rms-change max change #iterations 4.785214 185.1658 at 10iterations 2.402663 72.54247 at 20iterations 1.220730 34.93001 at 30iterations 0.6187585 17.56308 at 40iterations 0.3114466 9.241972 at 50iterations 0.1572812 5.071976 at 60iterations 7.9661481E-02 2.417145 at 70iterations 4.0384911E-02 1.152856 at 80iterations 2.0685317E-02 0.6289444 at 90iterations 1.0623161E-02 0.3081293 at 100iterations 5.5315024E-03 0.1776962 at 110iterations 2.9918586E-03 9.2464805E-02 at 120iterations finished qdiffx linear iterations at : 06:15:09 total time elapsed so far: 10.43000 # loops : 120 mean,max change (kT/e) : 2.9918586E-03 9.2464805E-02 energy calculations done at 10.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.60000 DelPhi exited at 06:15:09 10.601u 0.439s 0:11.34 97.2% 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 06:15:09 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2019 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.284537 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): 26.58600 72.12000 ymin,ymax (A): 44.26200 82.43400 zmin,zma (A): -60.83200 -12.05800 x,y,z range (A): 45.53400 38.17200 48.77399 scale (grids/A): 3.284537 object centre (A): 49.35300 63.34800 -36.44500 number of atom coordinates read : 2019 total number of charged atoms : 1889 net assigned charge : 4.500006 assigned positive charge : 305.7132 centred at (gu) : 89.74083 86.94577 83.59857 assigned negative charge : -301.2132 centred at (gu) : 90.38974 87.44379 83.56953 start vw surface at 0.1000000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 179133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17353 grid for indexing accessible points = 1.400000 m= 100615 mr = 132310 m= 44312 mr = 83805 m= 13820 mr = 36667 m= 2855 mr = 10729 m= 365 mr = 2061 m= 10 mr = 251 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.110000 number of dielectric boundary points 75288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.240000 number of grid points assigned charge 15112 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) : 2.189692 object centre at (A) : 49.35300 63.34800 -36.44500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6014189E-02 -7.8350799E-03 midg,1,midg; midg,igrid,midg 0.3594244 -4.8104834E-02 1,midg,midg; igrid,midg,midg 0.4108679 0.4143793 gauss-seidel spectral radius is 0.9993117 estimated iterations to convergence 301 setup time was (sec) 2.440000 now iterating at: 06:15:12 rms-change max change #iterations 10.54150 400.1539 at 10iterations 6.331283 190.4335 at 20iterations 3.782193 73.10758 at 30iterations 2.255412 40.11092 at 40iterations 1.344420 26.40436 at 50iterations 0.7949280 14.12516 at 60iterations 0.4715106 8.218273 at 70iterations 0.2795195 5.263584 at 80iterations 0.1652785 2.821424 at 90iterations 9.7467773E-02 1.579448 at 100iterations 5.7724897E-02 1.040010 at 110iterations 3.4348097E-02 0.6201019 at 120iterations 2.0660194E-02 0.3574219 at 130iterations 1.2632426E-02 0.2523022 at 140iterations 8.0133956E-03 0.1609306 at 150iterations 5.3547239E-03 0.1053925 at 160iterations 3.8247516E-03 7.0774078E-02 at 170iterations 2.9269850E-03 5.1288605E-02 at 180iterations finished qdiffx linear iterations at : 06:15:28 total time elapsed so far: 18.44000 # loops : 180 mean,max change (kT/e) : 2.9269850E-03 5.1288605E-02 energy calculations done at 18.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.60000 DelPhi exited at 06:15:29 18.605u 0.485s 0:19.69 96.9% 0+0k 0+0io 0pf+0w