Sat Oct 15 15:04:07 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 Sat Oct 15 2011 at 15:04:07 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2666 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 0.6665668 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): -21.53600 24.94500 ymin,ymax (A): 10.83100 64.23900 zmin,zma (A): -17.69600 30.20900 x,y,z range (A): 46.48100 53.40800 47.90500 scale (grids/A): 0.6665668 object centre (A): 1.704500 37.53500 6.256500 number of atom coordinates read : 2666 total number of charged atoms : 2531 net assigned charge : 3.000015 assigned positive charge : 410.8965 centred at (gu) : 89.20692 89.85880 90.33020 assigned negative charge : -407.8975 centred at (gu) : 89.36111 89.58155 90.38091 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7947 nv = 96 ne = 84 npr = 54787 no. pairs analyzed = 54787 no. exposed pairs = 3293 no. arc points = 22429 no. surface atoms = 1105 nbur = 1561 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 482 mr = 4559 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 72 time to turn everything in is 0.2000000 number of dielectric boundary points 3826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2107 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9329 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0029860E-08 -3.7636974E-09 midg,1,midg; midg,igrid,midg -6.2942455E-08 7.3010668E-08 1,midg,midg; igrid,midg,midg 5.4662493E-08 -2.4859746E-08 gauss-seidel spectral radius is 0.9883380 estimated iterations to convergence 76 setup time was (sec) 0.3900000 now iterating at: 15:04:08 rms-change max change #iterations 0.1811142 23.45860 at 10iterations 2.0384151E-02 2.657150 at 20iterations 3.0477364E-03 0.6087036 at 30iterations 8.4019598E-04 0.1831055 at 40iterations 2.9330398E-04 6.5879822E-02 at 50iterations finished qdiffx linear iterations at : 15:04:11 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 2.9330398E-04 6.5879822E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 15:04:12 3.537u 0.232s 0:04.24 88.6% 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 15:04:12 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2666 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 1.999701 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): -21.53600 24.94500 ymin,ymax (A): 10.83100 64.23900 zmin,zma (A): -17.69600 30.20900 x,y,z range (A): 46.48100 53.40800 47.90500 scale (grids/A): 1.999701 object centre (A): 1.704500 37.53500 6.256500 number of atom coordinates read : 2666 total number of charged atoms : 2531 net assigned charge : 3.000015 assigned positive charge : 410.8965 centred at (gu) : 87.62003 89.57566 90.99014 assigned negative charge : -407.8975 centred at (gu) : 88.08298 88.74429 91.14229 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22429 grid for indexing accessible points = 1.400000 m= 32202 mr = 60788 m= 5373 mr = 24114 m= 373 mr = 3532 m= 7 mr = 157 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2834 time to turn everything in is 0.4200000 number of dielectric boundary points 35124 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20030 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) : 0.6665668 object centre at (A) : 1.704500 37.53500 6.256500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3872955E-02 -2.3283912E-02 midg,1,midg; midg,igrid,midg -6.8151318E-02 7.0366912E-02 1,midg,midg; igrid,midg,midg 5.5725295E-02 -1.5800908E-02 gauss-seidel spectral radius is 0.9987644 estimated iterations to convergence 225 setup time was (sec) 0.6500000 now iterating at: 15:04:13 rms-change max change #iterations 4.835702 182.4867 at 10iterations 2.353766 80.28525 at 20iterations 1.141125 35.07324 at 30iterations 0.5544601 16.13798 at 40iterations 0.2697651 8.264425 at 50iterations 0.1307760 3.563095 at 60iterations 6.4024709E-02 1.985771 at 70iterations 3.1348810E-02 0.8905563 at 80iterations 1.5495614E-02 0.4623222 at 90iterations 7.8270519E-03 0.2421265 at 100iterations 4.0852721E-03 0.1453400 at 110iterations 2.2633334E-03 9.2163086E-02 at 120iterations finished qdiffx linear iterations at : 15:04:20 total time elapsed so far: 8.200000 # loops : 120 mean,max change (kT/e) : 2.2633334E-03 9.2163086E-02 energy calculations done at 8.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.340000 DelPhi exited at 15:04:21 8.340u 0.241s 0:09.33 91.9% 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 15:04:21 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2666 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 2.999551 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): -21.53600 24.94500 ymin,ymax (A): 10.83100 64.23900 zmin,zma (A): -17.69600 30.20900 x,y,z range (A): 46.48100 53.40800 47.90500 scale (grids/A): 2.999551 object centre (A): 1.704500 37.53500 6.256500 number of atom coordinates read : 2666 total number of charged atoms : 2531 net assigned charge : 3.000015 assigned positive charge : 410.8965 centred at (gu) : 86.42988 89.36335 91.48489 assigned negative charge : -407.8975 centred at (gu) : 87.12439 88.11643 91.71329 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 198249 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22429 grid for indexing accessible points = 1.400000 m= 102631 mr = 146493 m= 38721 mr = 84866 m= 9834 mr = 31727 m= 1616 mr = 7551 m= 129 mr = 1160 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 9499 time to turn everything in is 1.110000 number of dielectric boundary points 79317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 20247 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) : 1.999701 object centre at (A) : 1.704500 37.53500 6.256500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1910478 -0.2555469 midg,1,midg; midg,igrid,midg -0.7809987 0.9338583 1,midg,midg; igrid,midg,midg 0.4430721 -0.1751539 gauss-seidel spectral radius is 0.9992890 estimated iterations to convergence 296 setup time was (sec) 1.360000 now iterating at: 15:04:23 rms-change max change #iterations 11.08581 399.7744 at 10iterations 6.520514 146.2986 at 20iterations 3.831338 80.30317 at 30iterations 2.245979 46.78664 at 40iterations 1.313673 25.25509 at 50iterations 0.7681900 14.66813 at 60iterations 0.4487791 8.178623 at 70iterations 0.2616653 4.445412 at 80iterations 0.1527399 2.570831 at 90iterations 8.9025229E-02 1.535809 at 100iterations 5.1916633E-02 0.9702373 at 110iterations 3.0357299E-02 0.5610657 at 120iterations 1.7815504E-02 0.3387680 at 130iterations 1.0548295E-02 0.2066917 at 140iterations 6.3543143E-03 0.1277847 at 150iterations 3.9339657E-03 8.2744598E-02 at 160iterations 2.5563962E-03 5.8509827E-02 at 170iterations 1.7672953E-03 4.5486450E-02 at 180iterations finished qdiffx linear iterations at : 15:04:35 total time elapsed so far: 13.34000 # loops : 180 mean,max change (kT/e) : 1.7672953E-03 4.5486450E-02 energy calculations done at 13.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 15:04:35 13.478u 0.262s 0:14.32 95.8% 0+0k 0+0io 0pf+0w