Mon Oct 10 14:07:34 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 Mon Oct 10 2011 at 14:07:34 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 = 2289 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: 0.6897220 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): -20.10600 31.50900 ymin,ymax (A): -62.32200 -12.37100 zmin,zma (A): -8.168000 42.03300 x,y,z range (A): 51.61500 49.95100 50.20100 scale (grids/A): 0.6897220 object centre (A): 5.701500 -37.34650 16.93250 number of atom coordinates read : 2289 total number of charged atoms : 2154 net assigned charge : -4.499990 assigned positive charge : 342.1693 centred at (gu) : 89.15275 90.57735 89.62347 assigned negative charge : -346.6699 centred at (gu) : 89.35130 90.55354 89.56223 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7626 nv = 96 ne = 84 npr = 45834 no. pairs analyzed = 45834 no. exposed pairs = 3069 no. arc points = 21459 no. surface atoms = 1043 nbur = 1246 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 504 mr = 4091 m= 1 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3953 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1894 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8435 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1542191E-08 -2.8556293E-09 midg,1,midg; midg,igrid,midg -3.0377620E-08 -1.8455420E-08 1,midg,midg; igrid,midg,midg 5.5003117E-08 -8.3917172E-08 gauss-seidel spectral radius is 0.9890816 estimated iterations to convergence 78 setup time was (sec) 0.6500000 now iterating at: 14:07:35 rms-change max change #iterations 0.1880938 24.62426 at 10iterations 2.1894770E-02 3.109137 at 20iterations 2.5531831E-03 0.3811512 at 30iterations 3.0059094E-04 4.1160583E-02 at 40iterations 3.6888065E-05 4.8522949E-03 at 50iterations finished qdiffx linear iterations at : 14:07:38 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 3.6888065E-05 4.8522949E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 14:07:40 4.275u 0.239s 0:05.89 76.4% 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 Mon Oct 10 2011 at 14:07:40 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 = 2289 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: 2.069166 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): -20.10600 31.50900 ymin,ymax (A): -62.32200 -12.37100 zmin,zma (A): -8.168000 42.03300 x,y,z range (A): 51.61500 49.95100 50.20100 scale (grids/A): 2.069166 object centre (A): 5.701500 -37.34650 16.93250 number of atom coordinates read : 2289 total number of charged atoms : 2154 net assigned charge : -4.499990 assigned positive charge : 342.1693 centred at (gu) : 87.45808 91.73179 88.87008 assigned negative charge : -346.6699 centred at (gu) : 88.05389 91.66037 88.68665 start vw surface at 0.2100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 80635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21459 grid for indexing accessible points = 1.400000 m= 30928 mr = 54996 m= 5999 mr = 22810 m= 509 mr = 3887 m= 8 mr = 244 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 36142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 17118 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) : 0.6897220 object centre at (A) : 5.701500 -37.34650 16.93250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2858142E-02 -2.7736165E-02 midg,1,midg; midg,igrid,midg -9.6454350E-03 -1.3397838E-02 1,midg,midg; igrid,midg,midg -9.9541098E-03 -1.4526635E-02 gauss-seidel spectral radius is 0.9988157 estimated iterations to convergence 230 setup time was (sec) 1.170000 now iterating at: 14:07:42 rms-change max change #iterations 4.674911 260.0017 at 10iterations 2.284961 90.10124 at 20iterations 1.125736 36.70028 at 30iterations 0.5539116 18.81406 at 40iterations 0.2723420 8.878899 at 50iterations 0.1345324 4.124361 at 60iterations 6.6437386E-02 2.034800 at 70iterations 3.2703001E-02 0.9750690 at 80iterations 1.6073562E-02 0.4680557 at 90iterations 7.9429634E-03 0.2311249 at 100iterations 3.9233677E-03 0.1211090 at 110iterations 1.9336547E-03 5.4484367E-02 at 120iterations finished qdiffx linear iterations at : 14:07:50 total time elapsed so far: 9.650000 # loops : 120 mean,max change (kT/e) : 1.9336547E-03 5.4484367E-02 energy calculations done at 9.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.890000 DelPhi exited at 14:07:51 9.892u 0.258s 0:10.62 95.4% 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 Mon Oct 10 2011 at 14:07:51 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 = 2289 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: 3.103749 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): -20.10600 31.50900 ymin,ymax (A): -62.32200 -12.37100 zmin,zma (A): -8.168000 42.03300 x,y,z range (A): 51.61500 49.95100 50.20100 scale (grids/A): 3.103749 object centre (A): 5.701500 -37.34650 16.93250 number of atom coordinates read : 2289 total number of charged atoms : 2154 net assigned charge : -4.499990 assigned positive charge : 342.1693 centred at (gu) : 86.18705 92.59769 88.30508 assigned negative charge : -346.6699 centred at (gu) : 87.08091 92.49061 88.03001 start vw surface at 0.1700000 fill in re-entrant regions at 1.070000 boundary points on vw surface= 186014 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21459 grid for indexing accessible points = 1.400000 m= 96396 mr = 133293 m= 39049 mr = 78600 m= 11221 mr = 31521 m= 2165 mr = 8535 m= 202 mr = 1530 m= 10 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.440000 number of dielectric boundary points 81478 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.610000 number of grid points assigned charge 17232 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) : 2.069166 object centre at (A) : 5.701500 -37.34650 16.93250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1095334 -0.5288234 midg,1,midg; midg,igrid,midg -1.1493513E-05 2.2838651E-03 1,midg,midg; igrid,midg,midg -0.6008987 -3.7656266E-02 gauss-seidel spectral radius is 0.9993063 estimated iterations to convergence 300 setup time was (sec) 2.830000 now iterating at: 14:07:54 rms-change max change #iterations 10.72211 382.7981 at 10iterations 6.410934 134.0165 at 20iterations 3.827315 85.61112 at 30iterations 2.278718 46.47708 at 40iterations 1.349896 25.19305 at 50iterations 0.7989407 14.00952 at 60iterations 0.4718948 8.537521 at 70iterations 0.2777709 5.140517 at 80iterations 0.1634293 2.733898 at 90iterations 9.6075758E-02 1.620712 at 100iterations 5.6508690E-02 1.043450 at 110iterations 3.3090990E-02 0.6108036 at 120iterations 1.9446976E-02 0.3389874 at 130iterations 1.1406806E-02 0.1825867 at 140iterations 6.6907178E-03 0.1253108 at 150iterations 3.9350642E-03 6.9637299E-02 at 160iterations 2.3111277E-03 3.9243698E-02 at 170iterations 1.3595617E-03 2.3637772E-02 at 180iterations finished qdiffx linear iterations at : 14:08:09 total time elapsed so far: 17.58000 # loops : 180 mean,max change (kT/e) : 1.3595617E-03 2.3637772E-02 energy calculations done at 17.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.83000 DelPhi exited at 14:08:10 17.830u 0.291s 0:18.66 97.1% 0+0k 0+0io 0pf+0w