Wed Dec 28 11:02:07 PST 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 Wed Dec 28 2011 at 11:02:07 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 0.6946478 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): 78.11200 129.3610 ymin,ymax (A): -8.000000 42.73000 zmin,zma (A): -2.576000 46.83400 x,y,z range (A): 51.24899 50.73000 49.41000 scale (grids/A): 0.6946478 object centre (A): 103.7365 17.36500 22.12900 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 4.000005 assigned positive charge : 290.9100 centred at (gu) : 87.51870 90.05271 91.97290 assigned negative charge : -286.9103 centred at (gu) : 87.40025 90.03534 92.13737 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6566 nv = 96 ne = 84 npr = 40067 no. pairs analyzed = 40067 no. exposed pairs = 2578 no. arc points = 17978 no. surface atoms = 875 nbur = 1085 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 3606 m= 2 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2900000 number of dielectric boundary points 3309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1733 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7292 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5138688E-08 -4.4727184E-08 midg,1,midg; midg,igrid,midg 2.0904213E-08 3.3120507E-08 1,midg,midg; igrid,midg,midg -2.3444702E-08 4.0806952E-08 gauss-seidel spectral radius is 0.9891971 estimated iterations to convergence 78 setup time was (sec) 0.6300000 now iterating at: 11:02:08 rms-change max change #iterations 0.1785384 30.81169 at 10iterations 2.0655448E-02 3.055340 at 20iterations 2.4815137E-03 0.3891754 at 30iterations 2.9303334E-04 3.9594650E-02 at 40iterations 3.4175660E-05 4.9018860E-03 at 50iterations finished qdiffx linear iterations at : 11:02:13 total time elapsed so far: 5.150000 # loops : 50 mean,max change (kT/e) : 3.4175660E-05 4.9018860E-03 energy calculations done at 5.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.340000 DelPhi exited at 11:02:15 5.348u 0.420s 0:08.09 71.1% 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 Wed Dec 28 2011 at 11:02:16 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 2.083943 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): 78.11200 129.3610 ymin,ymax (A): -8.000000 42.73000 zmin,zma (A): -2.576000 46.83400 x,y,z range (A): 51.24899 50.73000 49.41000 scale (grids/A): 2.083943 object centre (A): 103.7365 17.36500 22.12900 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 4.000005 assigned positive charge : 290.9100 centred at (gu) : 82.55595 90.15807 95.91842 assigned negative charge : -286.9103 centred at (gu) : 82.20103 90.10615 96.41215 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 69242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17978 grid for indexing accessible points = 1.400000 m= 27148 mr = 47074 m= 5171 mr = 20907 m= 453 mr = 3630 m= 9 mr = 267 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 798 time to turn everything in is 0.6400000 number of dielectric boundary points 30145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 14520 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) : 0.6946478 object centre at (A) : 103.7365 17.36500 22.12900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6953151E-02 -1.9157901E-02 midg,1,midg; midg,igrid,midg 7.9282364E-03 6.1851373E-04 1,midg,midg; igrid,midg,midg -8.5949982E-03 5.1544692E-02 gauss-seidel spectral radius is 0.9987783 estimated iterations to convergence 227 setup time was (sec) 0.9300000 now iterating at: 11:02:17 rms-change max change #iterations 4.331715 186.6671 at 10iterations 2.110121 65.55246 at 20iterations 1.028793 34.07910 at 30iterations 0.5019139 15.60516 at 40iterations 0.2444209 7.514493 at 50iterations 0.1188230 3.940302 at 60iterations 5.7801172E-02 1.955868 at 70iterations 2.8263263E-02 0.9309174 at 80iterations 1.3756221E-02 0.4528441 at 90iterations 6.7112460E-03 0.1988192 at 100iterations 3.2715069E-03 9.9089622E-02 at 110iterations 1.5980860E-03 5.1964402E-02 at 120iterations finished qdiffx linear iterations at : 11:02:27 total time elapsed so far: 11.57000 # loops : 120 mean,max change (kT/e) : 1.5980860E-03 5.1964402E-02 energy calculations done at 11.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.76000 DelPhi exited at 11:02:29 11.761u 0.318s 0:13.01 92.7% 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 Wed Dec 28 2011 at 11:02:29 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 3.125915 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): 78.11200 129.3610 ymin,ymax (A): -8.000000 42.73000 zmin,zma (A): -2.576000 46.83400 x,y,z range (A): 51.24899 50.73000 49.41000 scale (grids/A): 3.125915 object centre (A): 103.7365 17.36500 22.12900 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 4.000005 assigned positive charge : 290.9100 centred at (gu) : 78.83389 90.23734 98.87750 assigned negative charge : -286.9103 centred at (gu) : 78.30166 90.15924 99.61839 start vw surface at 0.1400000 fill in re-entrant regions at 0.9300000 boundary points on vw surface= 159338 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17978 grid for indexing accessible points = 1.400000 m= 84094 mr = 113594 m= 34591 mr = 69896 m= 9736 mr = 29003 m= 2061 mr = 7931 m= 241 mr = 1664 m= 8 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 2469 time to turn everything in is 2.120000 number of dielectric boundary points 67820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 14624 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) : 2.083943 object centre at (A) : 103.7365 17.36500 22.12900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5362520 -0.2716482 midg,1,midg; midg,igrid,midg -4.1201949E-02 -7.5732872E-02 1,midg,midg; igrid,midg,midg -0.1289332 0.4378336 gauss-seidel spectral radius is 0.9992965 estimated iterations to convergence 297 setup time was (sec) 2.530000 now iterating at: 11:02:32 rms-change max change #iterations 9.833182 507.2789 at 10iterations 5.729675 137.6924 at 20iterations 3.382664 76.52075 at 30iterations 1.976947 41.18269 at 40iterations 1.153452 25.82040 at 50iterations 0.6715580 14.65764 at 60iterations 0.3919018 7.204414 at 70iterations 0.2277709 3.961521 at 80iterations 0.1328214 2.510154 at 90iterations 7.7106245E-02 1.604827 at 100iterations 4.4863082E-02 0.7967720 at 110iterations 2.6094435E-02 0.5228348 at 120iterations 1.5221390E-02 0.3029306 at 130iterations 8.8339346E-03 0.1557078 at 140iterations 5.1358412E-03 9.7092405E-02 at 150iterations 2.9919511E-03 5.6312561E-02 at 160iterations 1.7398911E-03 3.3140182E-02 at 170iterations 1.0138246E-03 1.8027782E-02 at 180iterations finished qdiffx linear iterations at : 11:02:51 total time elapsed so far: 21.51000 # loops : 180 mean,max change (kT/e) : 1.0138246E-03 1.8027782E-02 energy calculations done at 21.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.70000 DelPhi exited at 11:02:52 21.704u 0.529s 0:22.92 96.9% 0+0k 0+0io 0pf+0w