Tue Oct 11 07:18:25 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 07:18:25 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 = 3503 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: 0.5855456 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): 0.4610001 50.38300 ymin,ymax (A): -7.375000 52.14500 zmin,zma (A): 0.8779999 61.67600 x,y,z range (A): 49.92200 59.52000 60.79800 scale (grids/A): 0.5855456 object centre (A): 25.42200 22.38500 31.27700 number of atom coordinates read : 3503 total number of charged atoms : 3351 net assigned charge : -0.9999920 assigned positive charge : 529.8423 centred at (gu) : 89.68333 88.88750 89.96930 assigned negative charge : -530.8439 centred at (gu) : 89.56452 88.83584 89.96088 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7886 nv = 96 ne = 84 npr = 71718 no. pairs analyzed = 71718 no. exposed pairs = 4078 no. arc points = 27451 no. surface atoms = 1384 nbur = 2119 mkacc time = 0.1200000 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= 350 mr = 4604 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.2400000 number of dielectric boundary points 3607 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2827 ## 290 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 10009 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9710347E-10 3.6719221E-11 midg,1,midg; midg,igrid,midg -2.4270077E-09 1.0677110E-09 1,midg,midg; igrid,midg,midg -4.3370783E-09 3.2131522E-09 gauss-seidel spectral radius is 0.9849782 estimated iterations to convergence 67 setup time was (sec) 0.4300000 now iterating at: 07:18:26 rms-change max change #iterations 0.1117435 14.76233 at 10iterations 9.4052665E-03 1.379242 at 20iterations 8.6601300E-04 0.1283455 at 30iterations 1.2243319E-04 2.2247314E-02 at 40iterations 2.3878514E-05 4.5566559E-03 at 50iterations finished qdiffx linear iterations at : 07:18:28 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.3878514E-05 4.5566559E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 07:18:29 3.451u 0.183s 0:04.20 86.4% 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 Tue Oct 11 2011 at 07:18:29 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3503 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: 1.756637 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): 0.4610001 50.38300 ymin,ymax (A): -7.375000 52.14500 zmin,zma (A): 0.8779999 61.67600 x,y,z range (A): 49.92200 59.52000 60.79800 scale (grids/A): 1.756637 object centre (A): 25.42200 22.38500 31.27700 number of atom coordinates read : 3503 total number of charged atoms : 3351 net assigned charge : -0.9999920 assigned positive charge : 529.8423 centred at (gu) : 89.04897 86.66145 89.90688 assigned negative charge : -530.8439 centred at (gu) : 88.69318 86.50710 89.88228 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 87142 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27451 grid for indexing accessible points = 1.400000 m= 31426 mr = 63187 m= 3898 mr = 23911 m= 147 mr = 2357 m= 0 mr = 33 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 223 time to turn everything in is 0.4300000 number of dielectric boundary points 33125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 250 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 26055 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) : 0.5855456 object centre at (A) : 25.42200 22.38500 31.27700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5996931E-03 -3.3434379E-04 midg,1,midg; midg,igrid,midg -1.8559521E-02 -1.0217199E-02 1,midg,midg; igrid,midg,midg -1.6602887E-02 8.9059900E-03 gauss-seidel spectral radius is 0.9984835 estimated iterations to convergence 204 setup time was (sec) 0.6500000 now iterating at: 07:18:30 rms-change max change #iterations 4.314353 188.0121 at 10iterations 1.931661 66.27516 at 20iterations 0.8686473 31.21757 at 30iterations 0.3924002 12.60894 at 40iterations 0.1768188 5.247276 at 50iterations 7.9726949E-02 2.810198 at 60iterations 3.5934344E-02 1.130873 at 70iterations 1.6228572E-02 0.4716549 at 80iterations 7.3029506E-03 0.2358665 at 90iterations 3.3050033E-03 0.1046076 at 100iterations 1.4952819E-03 4.4304848E-02 at 110iterations 6.7403185E-04 2.1332264E-02 at 120iterations finished qdiffx linear iterations at : 07:18:37 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 6.7403185E-04 2.1332264E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 07:18:38 7.932u 0.207s 0:08.68 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 07:18:38 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 = 3503 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: 2.634955 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): 0.4610001 50.38300 ymin,ymax (A): -7.375000 52.14500 zmin,zma (A): 0.8779999 61.67600 x,y,z range (A): 49.92200 59.52000 60.79800 scale (grids/A): 2.634955 object centre (A): 25.42200 22.38500 31.27700 number of atom coordinates read : 3503 total number of charged atoms : 3351 net assigned charge : -0.9999920 assigned positive charge : 529.8423 centred at (gu) : 88.57330 84.99198 89.86004 assigned negative charge : -530.8439 centred at (gu) : 88.03967 84.76071 89.82336 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 201814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27451 grid for indexing accessible points = 1.400000 m= 104565 mr = 152516 m= 34889 mr = 87439 m= 6598 mr = 28459 m= 572 mr = 4893 m= 20 mr = 396 m= 0 mr = 12 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 693 time to turn everything in is 1.070000 number of dielectric boundary points 74743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 26796 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) : 1.756637 object centre at (A) : 25.42200 22.38500 31.27700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9112194E-02 -0.2432244 midg,1,midg; midg,igrid,midg -0.3939468 -0.1086604 1,midg,midg; igrid,midg,midg -0.1866157 9.7238421E-02 gauss-seidel spectral radius is 0.9992298 estimated iterations to convergence 284 setup time was (sec) 1.320000 now iterating at: 07:18:39 rms-change max change #iterations 10.53772 343.2110 at 10iterations 6.069004 122.3091 at 20iterations 3.479333 85.76385 at 30iterations 1.992348 49.38631 at 40iterations 1.139011 22.50427 at 50iterations 0.6503882 10.70771 at 60iterations 0.3709747 6.688480 at 70iterations 0.2112299 4.195211 at 80iterations 0.1201687 2.070686 at 90iterations 6.8465494E-02 1.159051 at 100iterations 3.8964830E-02 0.6734676 at 110iterations 2.2106878E-02 0.4241629 at 120iterations 1.2602596E-02 0.2279711 at 130iterations 7.1596177E-03 0.1268492 at 140iterations 4.0857918E-03 7.3888779E-02 at 150iterations 2.3284985E-03 4.1060448E-02 at 160iterations 1.3290173E-03 2.3677826E-02 at 170iterations 7.6267536E-04 1.2950897E-02 at 180iterations finished qdiffx linear iterations at : 07:18:51 total time elapsed so far: 12.80000 # loops : 180 mean,max change (kT/e) : 7.6267536E-04 1.2950897E-02 energy calculations done at 12.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 07:18:52 12.942u 0.205s 0:13.67 96.1% 0+0k 0+0io 0pf+0w