Sat Oct 15 15:08:46 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+sph.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 = amb.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 15:08:46 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2710 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6387941 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): -46.31100 0.9180000 ymin,ymax (A): -47.32700 1.559000 zmin,zma (A): -9.997001 45.73300 x,y,z range (A): 47.22900 48.88600 55.73000 scale (grids/A): 0.6387941 object centre (A): -22.69650 -22.88400 17.86800 number of atom coordinates read : 2710 total number of charged atoms : 2558 net assigned charge : 3.162012 assigned positive charge : 407.6968 centred at (gu) : 90.01987 90.41232 91.90324 assigned negative charge : -404.5354 centred at (gu) : 89.75567 90.21886 91.83665 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7365 nv = 96 ne = 84 npr = 55465 no. pairs analyzed = 55465 no. exposed pairs = 3281 no. arc points = 22812 no. surface atoms = 1092 nbur = 1618 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 4137 m= 1 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2100000 number of dielectric boundary points 3572 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2269 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8817 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3470057E-09 1.8090768E-08 midg,1,midg; midg,igrid,midg -1.7294296E-08 2.8906229E-08 1,midg,midg; igrid,midg,midg -2.7543193E-08 3.4468574E-08 gauss-seidel spectral radius is 0.9873095 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 15:08:46 rms-change max change #iterations 0.1469240 20.71410 at 10iterations 1.4671847E-02 1.874700 at 20iterations 1.5301002E-03 0.2139282 at 30iterations 2.1428465E-04 3.3290863E-02 at 40iterations 5.2181342E-05 6.8588257E-03 at 50iterations finished qdiffx linear iterations at : 15:08:50 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 5.2181342E-05 6.8588257E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 15:08:50 3.555u 0.207s 0:04.25 88.2% 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 15:08:50 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2710 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.916382 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): -46.31100 0.9180000 ymin,ymax (A): -47.32700 1.559000 zmin,zma (A): -9.997001 45.73300 x,y,z range (A): 47.22900 48.88600 55.73000 scale (grids/A): 1.916382 object centre (A): -22.69650 -22.88400 17.86800 number of atom coordinates read : 2710 total number of charged atoms : 2558 net assigned charge : 3.162012 assigned positive charge : 407.6968 centred at (gu) : 90.05920 91.23640 95.70914 assigned negative charge : -404.5354 centred at (gu) : 89.26657 90.65638 95.50939 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79403 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22812 grid for indexing accessible points = 1.400000 m= 30065 mr = 56130 m= 4927 mr = 22480 m= 327 mr = 3212 m= 7 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 592 time to turn everything in is 0.4100000 number of dielectric boundary points 32791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 20123 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) : 0.6387941 object centre at (A) : -22.69650 -22.88400 17.86800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6874185E-02 1.0512893E-02 midg,1,midg; midg,igrid,midg -1.0435000E-02 3.6022518E-02 1,midg,midg; igrid,midg,midg -1.6133826E-02 5.0324228E-02 gauss-seidel spectral radius is 0.9986605 estimated iterations to convergence 216 setup time was (sec) 0.6800000 now iterating at: 15:08:51 rms-change max change #iterations 4.393515 179.7104 at 10iterations 2.075290 77.71768 at 20iterations 0.9850382 32.11921 at 30iterations 0.4665688 15.54715 at 40iterations 0.2196997 7.063966 at 50iterations 0.1039893 2.972439 at 60iterations 4.9067426E-02 1.534767 at 70iterations 2.3246516E-02 0.7238464 at 80iterations 1.0966070E-02 0.3457298 at 90iterations 5.2153692E-03 0.1785765 at 100iterations 2.4744910E-03 7.4136257E-02 at 110iterations 1.1796074E-03 3.6735535E-02 at 120iterations finished qdiffx linear iterations at : 15:09:00 total time elapsed so far: 9.040000 # loops : 120 mean,max change (kT/e) : 1.1796074E-03 3.6735535E-02 energy calculations done at 9.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.170000 DelPhi exited at 15:09:00 9.175u 0.284s 0:10.04 94.1% 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 Sat Oct 15 2011 at 15:09:00 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2710 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.874574 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): -46.31100 0.9180000 ymin,ymax (A): -47.32700 1.559000 zmin,zma (A): -9.997001 45.73300 x,y,z range (A): 47.22900 48.88600 55.73000 scale (grids/A): 2.874574 object centre (A): -22.69650 -22.88400 17.86800 number of atom coordinates read : 2710 total number of charged atoms : 2558 net assigned charge : 3.162012 assigned positive charge : 407.6968 centred at (gu) : 90.08874 91.85443 98.56358 assigned negative charge : -404.5354 centred at (gu) : 88.89999 90.98447 98.26402 start vw surface at 0.1000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 183110 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22812 grid for indexing accessible points = 1.400000 m= 96055 mr = 135123 m= 36161 mr = 79527 m= 9066 mr = 29525 m= 1414 mr = 6891 m= 80 mr = 935 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 1855 time to turn everything in is 1.120000 number of dielectric boundary points 73850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 20456 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) : 1.916382 object centre at (A) : -22.69650 -22.88400 17.86800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3407232 0.3339501 midg,1,midg; midg,igrid,midg -0.1413110 0.4256949 1,midg,midg; igrid,midg,midg -0.1271989 0.4200982 gauss-seidel spectral radius is 0.9992633 estimated iterations to convergence 291 setup time was (sec) 1.420000 now iterating at: 15:09:02 rms-change max change #iterations 10.32343 436.9078 at 10iterations 6.078229 136.1896 at 20iterations 3.545112 74.26256 at 30iterations 2.066305 39.59679 at 40iterations 1.201540 24.96928 at 50iterations 0.6978191 12.91082 at 60iterations 0.4041564 7.525261 at 70iterations 0.2339225 4.402884 at 80iterations 0.1354741 2.553980 at 90iterations 7.8220628E-02 1.415086 at 100iterations 4.5189522E-02 0.8031769 at 110iterations 2.6194578E-02 0.4533024 at 120iterations 1.5177249E-02 0.2827835 at 130iterations 8.7737059E-03 0.1424370 at 140iterations 5.1105232E-03 9.5995903E-02 at 150iterations 3.0021404E-03 5.6999207E-02 at 160iterations 1.7908054E-03 3.2309175E-02 at 170iterations 1.0882866E-03 2.0084381E-02 at 180iterations finished qdiffx linear iterations at : 15:09:16 total time elapsed so far: 15.28000 # loops : 180 mean,max change (kT/e) : 1.0882866E-03 2.0084381E-02 energy calculations done at 15.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.40000 DelPhi exited at 15:09:17 15.406u 0.326s 0:16.20 97.0% 0+0k 0+0io 0pf+0w