Sun Oct 9 16:18:18 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 Sun Oct 9 2011 at 16:18:18 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3062 !!! WARNING: GLM 164 has a net charge of -0.0940 !!! WARNING: GLM 233 has a net charge of -0.0940 !!! WARNING: MG3 345 has a net charge of 1.4000 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: 0.6344002 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): -15.53900 37.16000 ymin,ymax (A): 54.22400 107.3640 zmin,zma (A): -4.495000 51.62100 x,y,z range (A): 52.69900 53.14000 56.11600 scale (grids/A): 0.6344002 object centre (A): 10.81050 80.79400 23.56300 number of atom coordinates read : 3062 total number of charged atoms : 2910 net assigned charge : -3.287975 assigned positive charge : 452.1791 centred at (gu) : 90.22041 88.78139 91.39291 assigned negative charge : -455.4685 centred at (gu) : 90.25178 88.66067 91.44365 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8127 nv = 96 ne = 84 npr = 63287 no. pairs analyzed = 63287 no. exposed pairs = 3645 no. arc points = 25760 no. surface atoms = 1232 nbur = 1830 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 455 mr = 4467 m= 3 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3500000 number of dielectric boundary points 4045 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2585 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9980 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5367643E-09 -1.3143103E-08 midg,1,midg; midg,igrid,midg -2.3577151E-08 7.7560225E-09 1,midg,midg; igrid,midg,midg -1.0123510E-10 -7.7886124E-09 gauss-seidel spectral radius is 0.9871687 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 16:18:19 rms-change max change #iterations 0.1556187 21.03104 at 10iterations 1.5014024E-02 1.886410 at 20iterations 1.4856246E-03 0.2258453 at 30iterations 1.5131259E-04 1.9140244E-02 at 40iterations 2.4145502E-05 4.1121244E-03 at 50iterations finished qdiffx linear iterations at : 16:18:22 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 2.4145502E-05 4.1121244E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 16:18:22 3.396u 0.157s 0:03.83 92.4% 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 Sun Oct 9 2011 at 16:18:22 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3062 !!! WARNING: GLM 164 has a net charge of -0.0940 !!! WARNING: GLM 233 has a net charge of -0.0940 !!! WARNING: MG3 345 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.903201 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): -15.53900 37.16000 ymin,ymax (A): 54.22400 107.3640 zmin,zma (A): -4.495000 51.62100 x,y,z range (A): 52.69900 53.14000 56.11600 scale (grids/A): 1.903201 object centre (A): 10.81050 80.79400 23.56300 number of atom coordinates read : 3062 total number of charged atoms : 2910 net assigned charge : -3.287975 assigned positive charge : 452.1791 centred at (gu) : 90.66074 86.34364 94.17769 assigned negative charge : -455.4685 centred at (gu) : 90.75509 85.98187 94.33057 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 88099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25760 grid for indexing accessible points = 1.400000 m= 31617 mr = 61607 m= 5479 mr = 23035 m= 372 mr = 3552 m= 8 mr = 141 m= 0 mr = 2 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 208 time to turn everything in is 0.6600000 number of dielectric boundary points 37238 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 22897 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) : 0.6344002 object centre at (A) : 10.81050 80.79400 23.56300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6432643E-02 8.1566954E-03 midg,1,midg; midg,igrid,midg -2.9698549E-02 -9.9727977E-03 1,midg,midg; igrid,midg,midg -3.4817744E-02 -2.4026345E-02 gauss-seidel spectral radius is 0.9986749 estimated iterations to convergence 218 setup time was (sec) 0.9700000 now iterating at: 16:18:23 rms-change max change #iterations 4.678015 204.4053 at 10iterations 2.205598 63.89869 at 20iterations 1.044372 31.07977 at 30iterations 0.4943245 14.57355 at 40iterations 0.2335146 6.802490 at 50iterations 0.1109434 3.482504 at 60iterations 5.2558698E-02 1.514556 at 70iterations 2.4791529E-02 0.7319183 at 80iterations 1.1802940E-02 0.3658252 at 90iterations 5.5995812E-03 0.1608620 at 100iterations 2.6630992E-03 7.9504013E-02 at 110iterations 1.2700537E-03 4.4685364E-02 at 120iterations finished qdiffx linear iterations at : 16:18:30 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 1.2700537E-03 4.4685364E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 16:18:30 7.591u 0.162s 0:08.03 96.5% 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 Sun Oct 9 2011 at 16:18:30 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3062 !!! WARNING: GLM 164 has a net charge of -0.0940 !!! WARNING: GLM 233 has a net charge of -0.0940 !!! WARNING: MG3 345 has a net charge of 1.4000 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: 2.854801 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): -15.53900 37.16000 ymin,ymax (A): 54.22400 107.3640 zmin,zma (A): -4.495000 51.62100 x,y,z range (A): 52.69900 53.14000 56.11600 scale (grids/A): 2.854801 object centre (A): 10.81050 80.79400 23.56300 number of atom coordinates read : 3062 total number of charged atoms : 2910 net assigned charge : -3.287975 assigned positive charge : 452.1791 centred at (gu) : 90.99088 84.51511 96.26630 assigned negative charge : -455.4685 centred at (gu) : 91.13261 83.97275 96.49586 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 204299 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25760 grid for indexing accessible points = 1.400000 m= 101312 mr = 149629 m= 38173 mr = 82476 m= 10106 mr = 30510 m= 1548 mr = 7701 m= 90 mr = 1027 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 726 time to turn everything in is 1.640000 number of dielectric boundary points 84143 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 23280 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) : 1.903201 object centre at (A) : 10.81050 80.79400 23.56300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5518144 0.2218499 midg,1,midg; midg,igrid,midg -0.3124315 -0.2649552 1,midg,midg; igrid,midg,midg -0.4994248 -0.2880915 gauss-seidel spectral radius is 0.9992777 estimated iterations to convergence 294 setup time was (sec) 1.950000 now iterating at: 16:18:32 rms-change max change #iterations 10.85599 409.9338 at 10iterations 6.385592 123.4327 at 20iterations 3.733552 75.96313 at 30iterations 2.175485 39.80389 at 40iterations 1.268094 25.26806 at 50iterations 0.7369912 14.00741 at 60iterations 0.4284477 7.439743 at 70iterations 0.2488772 4.582951 at 80iterations 0.1446154 2.546715 at 90iterations 8.3796859E-02 1.697745 at 100iterations 4.8619401E-02 0.8280401 at 110iterations 2.8165916E-02 0.4794064 at 120iterations 1.6304987E-02 0.2701206 at 130iterations 9.4640758E-03 0.1695099 at 140iterations 5.4740249E-03 9.4295502E-02 at 150iterations 3.1716097E-03 5.5002213E-02 at 160iterations 1.8364300E-03 2.9600620E-02 at 170iterations 1.0659248E-03 1.8434525E-02 at 180iterations finished qdiffx linear iterations at : 16:18:43 total time elapsed so far: 12.27000 # loops : 180 mean,max change (kT/e) : 1.0659248E-03 1.8434525E-02 energy calculations done at 12.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 16:18:43 12.466u 0.192s 0:12.94 97.7% 0+0k 0+0io 0pf+0w