Tue Oct 11 03:14:14 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 Tue Oct 11 2011 at 03:14:14 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 = 4361 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5197991 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): -9.672000 48.10400 ymin,ymax (A): 29.57200 88.18100 zmin,zma (A): 15.32000 83.80800 x,y,z range (A): 57.77600 58.60900 68.48800 scale (grids/A): 0.5197991 object centre (A): 19.21600 58.87650 49.56400 number of atom coordinates read : 4361 total number of charged atoms : 4210 net assigned charge : 1.3470650E-05 assigned positive charge : 667.3719 centred at (gu) : 90.30930 90.92697 91.15079 assigned negative charge : -667.3760 centred at (gu) : 90.27045 90.87486 91.14528 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7299 nv = 96 ne = 84 npr = 90137 no. pairs analyzed = 90137 no. exposed pairs = 5172 no. arc points = 35435 no. surface atoms = 1736 nbur = 2625 mkacc time = 0.3000000 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= 248 mr = 3934 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.3499999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 3600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3414 ## 451 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 9775 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6499854E-11 2.2969772E-11 midg,1,midg; midg,igrid,midg -1.4863388E-10 2.3211974E-10 1,midg,midg; igrid,midg,midg -1.3061539E-10 1.4640322E-10 gauss-seidel spectral radius is 0.9810315 estimated iterations to convergence 60 setup time was (sec) 0.8900000 now iterating at: 03:14:16 rms-change max change #iterations 7.4231856E-02 13.55383 at 10iterations 4.6713687E-03 0.7323418 at 20iterations 5.8575976E-04 7.8311920E-02 at 30iterations 1.6435384E-04 2.2085190E-02 at 40iterations 5.0179104E-05 6.7729950E-03 at 50iterations finished qdiffx linear iterations at : 03:14:19 total time elapsed so far: 4.520000 # loops : 50 mean,max change (kT/e) : 5.0179104E-05 6.7729950E-03 energy calculations done at 4.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.740000 DelPhi exited at 03:14:20 4.744u 0.398s 0:05.47 93.7% 0+0k 0+0io 4pf+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 03:14:20 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 = 4361 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.559397 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): -9.672000 48.10400 ymin,ymax (A): 29.57200 88.18100 zmin,zma (A): 15.32000 83.80800 x,y,z range (A): 57.77600 58.60900 68.48800 scale (grids/A): 1.559397 object centre (A): 19.21600 58.87650 49.56400 number of atom coordinates read : 4361 total number of charged atoms : 4210 net assigned charge : 1.3470650E-05 assigned positive charge : 667.3719 centred at (gu) : 90.92616 92.77964 93.45055 assigned negative charge : -667.3760 centred at (gu) : 90.81074 92.62411 93.43541 start vw surface at 0.2100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 81851 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35435 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 24241 mr = 57114 m= 2343 mr = 16897 m= 31 mr = 1105 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 1781 time to turn everything in is 0.8400000 number of dielectric boundary points 33351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 386 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 31803 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) : 0.5197991 object centre at (A) : 19.21600 58.87650 49.56400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5716056E-03 -2.9064124E-03 midg,1,midg; midg,igrid,midg 5.1564397E-03 1.3027401E-02 1,midg,midg; igrid,midg,midg -2.0105613E-03 -3.2109874E-03 gauss-seidel spectral radius is 0.9981359 estimated iterations to convergence 184 setup time was (sec) 1.180000 now iterating at: 03:14:22 rms-change max change #iterations 3.828977 198.5410 at 10iterations 1.568853 55.03193 at 20iterations 0.6486706 20.08972 at 30iterations 0.2672040 9.265854 at 40iterations 0.1106497 3.446186 at 50iterations 4.5556396E-02 1.519329 at 60iterations 1.8963661E-02 0.6405258 at 70iterations 7.8522982E-03 0.2674561 at 80iterations 3.2917194E-03 0.1192322 at 90iterations 1.3937189E-03 4.6390533E-02 at 100iterations 6.1148702E-04 2.0076752E-02 at 110iterations 2.8203463E-04 9.8218918E-03 at 120iterations finished qdiffx linear iterations at : 03:14:31 total time elapsed so far: 10.29000 # loops : 120 mean,max change (kT/e) : 2.8203463E-04 9.8218918E-03 energy calculations done at 10.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.50000 DelPhi exited at 03:14:31 10.509u 0.466s 0:11.53 95.0% 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 03:14:31 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 = 4361 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.339096 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): -9.672000 48.10400 ymin,ymax (A): 29.57200 88.18100 zmin,zma (A): 15.32000 83.80800 x,y,z range (A): 57.77600 58.60900 68.48800 scale (grids/A): 2.339096 object centre (A): 19.21600 58.87650 49.56400 number of atom coordinates read : 4361 total number of charged atoms : 4210 net assigned charge : 1.3470650E-05 assigned positive charge : 667.3719 centred at (gu) : 91.38892 94.16908 95.17534 assigned negative charge : -667.3760 centred at (gu) : 91.21608 93.93614 95.15303 start vw surface at 0.2300000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 191255 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35435 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 85640 mr = 140234 m= 23279 mr = 68315 m= 3582 mr = 17714 m= 180 mr = 2268 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 6128 time to turn everything in is 2.060000 number of dielectric boundary points 75357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 33608 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) : 1.559397 object centre at (A) : 19.21600 58.87650 49.56400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8551908E-02 1.7581172E-02 midg,1,midg; midg,igrid,midg 0.1239220 0.1996697 1,midg,midg; igrid,midg,midg -7.8770891E-03 -7.8923717E-02 gauss-seidel spectral radius is 0.9991543 estimated iterations to convergence 272 setup time was (sec) 2.410000 now iterating at: 03:14:34 rms-change max change #iterations 10.02168 256.6556 at 10iterations 5.667991 132.7238 at 20iterations 3.190182 86.31375 at 30iterations 1.790413 36.61591 at 40iterations 1.000692 21.36390 at 50iterations 0.5576317 13.12267 at 60iterations 0.3100478 5.807545 at 70iterations 0.1727173 3.554636 at 80iterations 9.5986843E-02 2.798172 at 90iterations 5.3204000E-02 1.013844 at 100iterations 2.9602362E-02 0.6109924 at 110iterations 1.6445601E-02 0.3471069 at 120iterations 9.1330074E-03 0.2037735 at 130iterations 5.0685531E-03 0.1017218 at 140iterations 2.8288083E-03 5.7756424E-02 at 150iterations 1.5866366E-03 3.3058167E-02 at 160iterations 8.9662446E-04 1.6561508E-02 at 170iterations 5.1263045E-04 1.0303020E-02 at 180iterations finished qdiffx linear iterations at : 03:14:50 total time elapsed so far: 17.55000 # loops : 180 mean,max change (kT/e) : 5.1263045E-04 1.0303020E-02 energy calculations done at 17.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.77000 DelPhi exited at 03:14:50 17.775u 0.471s 0:18.65 97.8% 0+0k 0+0io 0pf+0w