Sat Oct 15 11:26:54 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 Sat Oct 15 2011 at 11:26:54 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4333 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: 0.5167959 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): 14.27100 70.33000 ymin,ymax (A): 34.67700 103.5630 zmin,zma (A): 22.99500 85.48400 x,y,z range (A): 56.05900 68.88600 62.48900 scale (grids/A): 0.5167959 object centre (A): 42.30050 69.12000 54.23950 number of atom coordinates read : 4333 total number of charged atoms : 4170 net assigned charge : -11.49995 assigned positive charge : 653.8972 centred at (gu) : 89.56104 90.24959 89.08736 assigned negative charge : -665.4009 centred at (gu) : 89.51498 90.23880 89.08820 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7515 nv = 96 ne = 84 npr = 84284 no. pairs analyzed = 84284 no. exposed pairs = 6069 no. arc points = 42898 no. surface atoms = 2006 nbur = 2327 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 = 1.652000 m= 289 mr = 3607 m= 0 mr = 5 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4039 ## 564 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 9987 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6635222E-10 -1.7199109E-10 midg,1,midg; midg,igrid,midg -2.3248060E-10 -1.9164387E-10 1,midg,midg; igrid,midg,midg -4.0238871E-10 -6.3456698E-11 gauss-seidel spectral radius is 0.9808313 estimated iterations to convergence 60 setup time was (sec) 0.4900000 now iterating at: 11:26:55 rms-change max change #iterations 6.8322606E-02 11.75544 at 10iterations 4.0651280E-03 0.7064624 at 20iterations 3.6901311E-04 5.9743226E-02 at 30iterations 8.7172986E-05 1.3706684E-02 at 40iterations 2.6470185E-05 3.8962364E-03 at 50iterations finished qdiffx linear iterations at : 11:26:58 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 2.6470185E-05 3.8962364E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 11:26:58 3.595u 0.226s 0:04.13 92.2% 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 Sat Oct 15 2011 at 11:26:58 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4333 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: 1.550388 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): 14.27100 70.33000 ymin,ymax (A): 34.67700 103.5630 zmin,zma (A): 22.99500 85.48400 x,y,z range (A): 56.05900 68.88600 62.48900 scale (grids/A): 1.550388 object centre (A): 42.30050 69.12000 54.23950 number of atom coordinates read : 4333 total number of charged atoms : 4170 net assigned charge : -11.49995 assigned positive charge : 653.8972 centred at (gu) : 88.68188 90.74731 87.26092 assigned negative charge : -665.4009 centred at (gu) : 88.54482 90.71638 87.26414 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83979 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42898 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 23894 mr = 54918 m= 2144 mr = 14963 m= 49 mr = 842 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 39344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 567 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 31380 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) : 0.5167959 object centre at (A) : 42.30050 69.12000 54.23950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4734952E-02 3.5719746E-03 midg,1,midg; midg,igrid,midg -1.3452603E-02 -1.6597202E-02 1,midg,midg; igrid,midg,midg -1.3106912E-02 -1.3587229E-02 gauss-seidel spectral radius is 0.9981457 estimated iterations to convergence 185 setup time was (sec) 0.6200000 now iterating at: 11:26:59 rms-change max change #iterations 3.735496 152.2667 at 10iterations 1.532745 51.90149 at 20iterations 0.6327478 21.86601 at 30iterations 0.2602085 8.096382 at 40iterations 0.1076888 3.401626 at 50iterations 4.4433534E-02 1.590500 at 60iterations 1.8380901E-02 0.6684418 at 70iterations 7.6542888E-03 0.2698708 at 80iterations 3.2004011E-03 0.1045876 at 90iterations 1.3661180E-03 4.5063496E-02 at 100iterations 6.1051897E-04 1.9660950E-02 at 110iterations 2.9404453E-04 1.0131836E-02 at 120iterations finished qdiffx linear iterations at : 11:27:07 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 2.9404453E-04 1.0131836E-02 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 11:27:07 8.174u 0.249s 0:09.01 93.3% 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 Sat Oct 15 2011 at 11:27:08 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4333 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: 2.325581 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): 14.27100 70.33000 ymin,ymax (A): 34.67700 103.5630 zmin,zma (A): 22.99500 85.48400 x,y,z range (A): 56.05900 68.88600 62.48900 scale (grids/A): 2.325581 object centre (A): 42.30050 69.12000 54.23950 number of atom coordinates read : 4333 total number of charged atoms : 4170 net assigned charge : -11.49995 assigned positive charge : 653.8972 centred at (gu) : 88.02249 91.12080 85.89113 assigned negative charge : -665.4009 centred at (gu) : 87.81717 91.07453 85.89627 start vw surface at 0.1200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 195362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42898 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 85408 mr = 135695 m= 21495 mr = 64208 m= 3055 mr = 14831 m= 187 mr = 1682 m= 6 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.010000 number of dielectric boundary points 89032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 33262 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) : 1.550388 object centre at (A) : 42.30050 69.12000 54.23950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3444362 0.1310925 midg,1,midg; midg,igrid,midg -0.1783700 -0.3750694 1,midg,midg; igrid,midg,midg -0.2265317 -0.2849295 gauss-seidel spectral radius is 0.9991761 estimated iterations to convergence 275 setup time was (sec) 1.280000 now iterating at: 11:27:09 rms-change max change #iterations 10.23376 300.2137 at 10iterations 5.937746 139.3553 at 20iterations 3.423905 90.86592 at 30iterations 1.954127 43.72263 at 40iterations 1.109547 24.52900 at 50iterations 0.6277441 13.91301 at 60iterations 0.3551071 7.725483 at 70iterations 0.1999325 4.199348 at 80iterations 0.1123627 2.190354 at 90iterations 6.3069269E-02 1.249300 at 100iterations 3.5335157E-02 0.8971405 at 110iterations 1.9801240E-02 0.3750420 at 120iterations 1.1068784E-02 0.2218552 at 130iterations 6.2063122E-03 0.1212177 at 140iterations 3.4813152E-03 8.0127716E-02 at 150iterations 1.9525078E-03 3.7705421E-02 at 160iterations 1.1016775E-03 2.1957397E-02 at 170iterations 6.2563596E-04 1.1957169E-02 at 180iterations finished qdiffx linear iterations at : 11:27:21 total time elapsed so far: 13.29000 # loops : 180 mean,max change (kT/e) : 6.2563596E-04 1.1957169E-02 energy calculations done at 13.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.42000 DelPhi exited at 11:27:22 13.420u 0.249s 0:14.14 96.6% 0+0k 0+0io 0pf+0w