Tue Oct 11 07:33:55 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 07:33:56 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3239 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5927801 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): 0.2609999 49.12400 ymin,ymax (A): -8.408999 49.36400 zmin,zma (A): 1.078000 61.13400 x,y,z range (A): 48.86300 57.77300 60.05600 scale (grids/A): 0.5927801 object centre (A): 24.69250 20.47750 31.10600 number of atom coordinates read : 3239 total number of charged atoms : 3074 net assigned charge : -3.099989 assigned positive charge : 484.9698 centred at (gu) : 89.56577 89.43631 90.74040 assigned negative charge : -488.0709 centred at (gu) : 89.52888 89.37157 90.67378 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7452 nv = 96 ne = 84 npr = 66876 no. pairs analyzed = 66876 no. exposed pairs = 3850 no. arc points = 26433 no. surface atoms = 1300 nbur = 1939 mkacc time = 0.1400000 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 = 1.456000 m= 382 mr = 4301 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 75 time to turn everything in is 0.3300000 number of dielectric boundary points 3500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2548 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9357 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9523912E-09 1.6461588E-09 midg,1,midg; midg,igrid,midg -3.9062567E-09 1.1399182E-09 1,midg,midg; igrid,midg,midg -2.6490490E-09 2.6615465E-10 gauss-seidel spectral radius is 0.9853224 estimated iterations to convergence 68 setup time was (sec) 0.5800000 now iterating at: 07:33:56 rms-change max change #iterations 0.1186788 20.71156 at 10iterations 1.0595747E-02 1.437988 at 20iterations 1.2357491E-03 0.1896763 at 30iterations 2.8738225E-04 4.6531677E-02 at 40iterations 8.1166218E-05 1.3439178E-02 at 50iterations finished qdiffx linear iterations at : 07:33:59 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 8.1166218E-05 1.3439178E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 07:33:59 3.414u 0.185s 0:03.95 90.8% 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 07:34:00 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3239 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.778340 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): 0.2609999 49.12400 ymin,ymax (A): -8.408999 49.36400 zmin,zma (A): 1.078000 61.13400 x,y,z range (A): 48.86300 57.77300 60.05600 scale (grids/A): 1.778340 object centre (A): 24.69250 20.47750 31.10600 number of atom coordinates read : 3239 total number of charged atoms : 3074 net assigned charge : -3.099989 assigned positive charge : 484.9698 centred at (gu) : 88.69641 88.30791 92.22058 assigned negative charge : -488.0709 centred at (gu) : 88.58629 88.11417 92.02069 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 82045 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26433 grid for indexing accessible points = 1.400000 m= 29744 mr = 58635 m= 4010 mr = 22532 m= 158 mr = 2493 m= 0 mr = 46 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 2384 time to turn everything in is 0.6100000 number of dielectric boundary points 32251 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 23915 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) : 0.5927801 object centre at (A) : 24.69250 20.47750 31.10600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5620753E-02 8.7670161E-04 midg,1,midg; midg,igrid,midg -1.8462468E-02 7.4195992E-03 1,midg,midg; igrid,midg,midg -1.3236614E-02 -4.8452117E-03 gauss-seidel spectral radius is 0.9984996 estimated iterations to convergence 205 setup time was (sec) 0.9000000 now iterating at: 07:34:01 rms-change max change #iterations 4.213791 177.1996 at 10iterations 1.899011 67.82495 at 20iterations 0.8599719 26.47909 at 30iterations 0.3899453 12.67988 at 40iterations 0.1767133 5.119918 at 50iterations 8.0197886E-02 2.945595 at 60iterations 3.6336381E-02 1.177353 at 70iterations 1.6499462E-02 0.5316124 at 80iterations 7.4857660E-03 0.2580605 at 90iterations 3.4456337E-03 0.1119690 at 100iterations 1.6083622E-03 5.4608345E-02 at 110iterations 7.6288427E-04 2.4183273E-02 at 120iterations finished qdiffx linear iterations at : 07:34:07 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 7.6288427E-04 2.4183273E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 07:34:08 7.598u 0.261s 0:08.25 95.1% 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 Tue Oct 11 2011 at 07:34:08 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3239 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.667510 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): 0.2609999 49.12400 ymin,ymax (A): -8.408999 49.36400 zmin,zma (A): 1.078000 61.13400 x,y,z range (A): 48.86300 57.77300 60.05600 scale (grids/A): 2.667510 object centre (A): 24.69250 20.47750 31.10600 number of atom coordinates read : 3239 total number of charged atoms : 3074 net assigned charge : -3.099989 assigned positive charge : 484.9698 centred at (gu) : 88.04425 87.46169 93.33070 assigned negative charge : -488.0709 centred at (gu) : 87.87934 87.17095 93.03098 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 190236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26433 grid for indexing accessible points = 1.400000 m= 98034 mr = 142031 m= 33652 mr = 81763 m= 6899 mr = 27455 m= 787 mr = 5162 m= 41 mr = 505 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 7889 time to turn everything in is 1.460000 number of dielectric boundary points 72729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 24580 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) : 1.778340 object centre at (A) : 24.69250 20.47750 31.10600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3902205 -0.2378609 midg,1,midg; midg,igrid,midg -0.3585933 0.1043270 1,midg,midg; igrid,midg,midg -0.1457884 -6.3801348E-02 gauss-seidel spectral radius is 0.9992304 estimated iterations to convergence 285 setup time was (sec) 1.760000 now iterating at: 07:34:10 rms-change max change #iterations 10.19999 280.4631 at 10iterations 5.868759 154.5330 at 20iterations 3.365475 70.01370 at 30iterations 1.922160 38.65210 at 40iterations 1.097622 22.07231 at 50iterations 0.6272573 11.69349 at 60iterations 0.3568241 7.823711 at 70iterations 0.2035393 4.121471 at 80iterations 0.1158366 2.649529 at 90iterations 6.5968812E-02 1.299082 at 100iterations 3.7566729E-02 0.6318235 at 110iterations 2.1360273E-02 0.3971920 at 120iterations 1.2171118E-02 0.2214737 at 130iterations 6.9626053E-03 0.1234550 at 140iterations 3.9833202E-03 7.4258804E-02 at 150iterations 2.3005435E-03 4.0592194E-02 at 160iterations 1.3412135E-03 2.3582458E-02 at 170iterations 7.9673057E-04 1.4528513E-02 at 180iterations finished qdiffx linear iterations at : 07:34:20 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 7.9673057E-04 1.4528513E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 07:34:21 12.596u 0.249s 0:13.14 97.6% 0+0k 0+0io 0pf+0w