Tue Oct 11 04:47:15 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 04:47:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2234 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6355100 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): 0.4910001 56.50900 ymin,ymax (A): -19.52300 23.19500 zmin,zma (A): -30.52600 19.43000 x,y,z range (A): 56.01800 42.71800 49.95600 scale (grids/A): 0.6355100 object centre (A): 28.50000 1.836000 -5.547999 number of atom coordinates read : 2234 total number of charged atoms : 2098 net assigned charge : 4.500010 assigned positive charge : 329.4146 centred at (gu) : 90.85059 90.68886 89.92236 assigned negative charge : -324.9149 centred at (gu) : 90.98779 90.88690 89.89088 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6093 nv = 96 ne = 84 npr = 44672 no. pairs analyzed = 44672 no. exposed pairs = 2859 no. arc points = 20688 no. surface atoms = 964 nbur = 1270 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 311 mr = 3194 m= 5 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.2800000 number of dielectric boundary points 3181 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2000 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7249 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3530136E-09 8.5861060E-09 midg,1,midg; midg,igrid,midg 1.9595824E-08 -1.3362128E-08 1,midg,midg; igrid,midg,midg 1.4727367E-08 -7.2940658E-09 gauss-seidel spectral radius is 0.9871440 estimated iterations to convergence 72 setup time was (sec) 0.5000000 now iterating at: 04:47:15 rms-change max change #iterations 0.1275742 22.33862 at 10iterations 1.2470178E-02 1.824730 at 20iterations 1.1980971E-03 0.1959896 at 30iterations 1.1710067E-04 1.8640518E-02 at 40iterations 1.1370747E-05 1.7147064E-03 at 50iterations finished qdiffx linear iterations at : 04:47:18 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.1370747E-05 1.7147064E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 04:47:19 3.316u 0.191s 0:04.15 84.3% 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 04:47:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2234 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.906530 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): 0.4910001 56.50900 ymin,ymax (A): -19.52300 23.19500 zmin,zma (A): -30.52600 19.43000 x,y,z range (A): 56.01800 42.71800 49.95600 scale (grids/A): 1.906530 object centre (A): 28.50000 1.836000 -5.547999 number of atom coordinates read : 2234 total number of charged atoms : 2098 net assigned charge : 4.500010 assigned positive charge : 329.4146 centred at (gu) : 92.55144 92.06617 89.76683 assigned negative charge : -324.9149 centred at (gu) : 92.96320 92.66067 89.67252 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 65361 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20688 grid for indexing accessible points = 1.400000 m= 22600 mr = 44160 m= 3424 mr = 16185 m= 209 mr = 2070 m= 4 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1661 time to turn everything in is 0.5000000 number of dielectric boundary points 29119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 95 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 16494 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) : 0.6355100 object centre at (A) : 28.50000 1.836000 -5.547999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0917311E-02 8.0593340E-03 midg,1,midg; midg,igrid,midg 2.1559760E-02 -9.0666460E-03 1,midg,midg; igrid,midg,midg 5.9562940E-02 3.1647237E-03 gauss-seidel spectral radius is 0.9986042 estimated iterations to convergence 212 setup time was (sec) 0.7900000 now iterating at: 04:47:20 rms-change max change #iterations 3.842016 169.5060 at 10iterations 1.779475 68.22240 at 20iterations 0.8266736 33.01495 at 30iterations 0.3820446 13.43828 at 40iterations 0.1774169 6.260686 at 50iterations 8.1955388E-02 2.795081 at 60iterations 3.8186021E-02 1.410431 at 70iterations 1.7647943E-02 0.6721792 at 80iterations 8.2013169E-03 0.2689981 at 90iterations 3.8200330E-03 0.1425362 at 100iterations 1.7706631E-03 6.0197353E-02 at 110iterations 8.2412356E-04 2.6387691E-02 at 120iterations finished qdiffx linear iterations at : 04:47:26 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 8.2412356E-04 2.6387691E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 04:47:27 7.535u 0.232s 0:08.33 93.1% 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 04:47:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2234 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.859795 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): 0.4910001 56.50900 ymin,ymax (A): -19.52300 23.19500 zmin,zma (A): -30.52600 19.43000 x,y,z range (A): 56.01800 42.71800 49.95600 scale (grids/A): 2.859795 object centre (A): 28.50000 1.836000 -5.547999 number of atom coordinates read : 2234 total number of charged atoms : 2098 net assigned charge : 4.500010 assigned positive charge : 329.4146 centred at (gu) : 93.82690 93.09916 89.65017 assigned negative charge : -324.9149 centred at (gu) : 94.44482 93.99108 89.50878 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 151053 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20688 grid for indexing accessible points = 1.400000 m= 73911 mr = 107178 m= 25694 mr = 59510 m= 6110 mr = 20137 m= 834 mr = 4455 m= 36 mr = 536 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 5886 time to turn everything in is 1.190000 number of dielectric boundary points 65811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 16780 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) : 1.906530 object centre at (A) : 28.50000 1.836000 -5.547999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1429890 8.7079994E-02 midg,1,midg; midg,igrid,midg 0.2196256 -5.6142293E-02 1,midg,midg; igrid,midg,midg 0.8922293 -0.2373791 gauss-seidel spectral radius is 0.9992509 estimated iterations to convergence 288 setup time was (sec) 1.490000 now iterating at: 04:47:29 rms-change max change #iterations 9.121435 640.5151 at 10iterations 5.320676 123.2859 at 20iterations 3.084581 76.86017 at 30iterations 1.781274 38.29630 at 40iterations 1.026564 21.70195 at 50iterations 0.5901116 12.46903 at 60iterations 0.3388744 6.893022 at 70iterations 0.1943970 3.824158 at 80iterations 0.1115078 2.183218 at 90iterations 6.3819796E-02 1.408020 at 100iterations 3.6587164E-02 0.7719574 at 110iterations 2.0928664E-02 0.4145241 at 120iterations 1.2017978E-02 0.2223232 at 130iterations 6.8678893E-03 0.1354752 at 140iterations 3.9230273E-03 7.5311661E-02 at 150iterations 2.2510020E-03 4.6808243E-02 at 160iterations 1.2852220E-03 2.3313284E-02 at 170iterations 7.3473505E-04 1.3694763E-02 at 180iterations finished qdiffx linear iterations at : 04:47:40 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 7.3473505E-04 1.3694763E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.26000 DelPhi exited at 04:47:40 12.262u 0.227s 0:13.25 94.1% 0+0k 0+0io 0pf+0w