Tue Oct 11 03:40:10 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 03:40:11 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3185 !!! WARNING: HIZ 79 has a net charge of 0.2000 !!! WARNING: GLU 288 has a net charge of -2.0000 !!! WARNING: ZN3 300 has a net charge of 1.4000 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6041270 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): -11.14500 36.88800 ymin,ymax (A): -27.30600 21.40400 zmin,zma (A): -13.40700 45.52100 x,y,z range (A): 48.03300 48.71000 58.92800 scale (grids/A): 0.6041270 object centre (A): 12.87150 -2.951000 16.05700 number of atom coordinates read : 3185 total number of charged atoms : 2769 net assigned charge : -1.759978 assigned positive charge : 443.5083 centred at (gu) : 89.91357 90.88552 92.41238 assigned negative charge : -445.2691 centred at (gu) : 89.70584 90.84859 92.28956 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7013 nv = 96 ne = 84 npr = 60126 no. pairs analyzed = 60126 no. exposed pairs = 3439 no. arc points = 24049 no. surface atoms = 1163 nbur = 2022 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 318 mr = 3954 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 60 time to turn everything in is 0.3100000 number of dielectric boundary points 3347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2522 ## 285 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8807 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9994945E-09 8.3122806E-09 midg,1,midg; midg,igrid,midg -2.2576379E-09 9.0787655E-10 1,midg,midg; igrid,midg,midg -1.1269949E-08 8.4017726E-09 gauss-seidel spectral radius is 0.9858386 estimated iterations to convergence 69 setup time was (sec) 0.5500000 now iterating at: 03:40:11 rms-change max change #iterations 0.1199508 20.37821 at 10iterations 1.0281161E-02 1.490646 at 20iterations 9.3120767E-04 0.1291847 at 30iterations 8.9637622E-05 1.3637543E-02 at 40iterations 1.1964551E-05 2.1705627E-03 at 50iterations finished qdiffx linear iterations at : 03:40:14 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 1.1964551E-05 2.1705627E-03 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 03:40:14 3.224u 0.165s 0:03.79 89.1% 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 03:40:14 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3185 !!! WARNING: HIZ 79 has a net charge of 0.2000 !!! WARNING: GLU 288 has a net charge of -2.0000 !!! WARNING: ZN3 300 has a net charge of 1.4000 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.812381 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): -11.14500 36.88800 ymin,ymax (A): -27.30600 21.40400 zmin,zma (A): -13.40700 45.52100 x,y,z range (A): 48.03300 48.71000 58.92800 scale (grids/A): 1.812381 object centre (A): 12.87150 -2.951000 16.05700 number of atom coordinates read : 3185 total number of charged atoms : 2769 net assigned charge : -1.759978 assigned positive charge : 443.5083 centred at (gu) : 89.74007 92.65584 97.23648 assigned negative charge : -445.2691 centred at (gu) : 89.11717 92.54536 96.86825 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76238 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24049 grid for indexing accessible points = 1.400000 m= 27235 mr = 53902 m= 3603 mr = 20346 m= 159 mr = 2082 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 3076 time to turn everything in is 0.5400000 number of dielectric boundary points 30862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21603 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) : 0.6041270 object centre at (A) : 12.87150 -2.951000 16.05700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5140674E-02 5.7708160E-03 midg,1,midg; midg,igrid,midg -4.0878146E-03 -1.6201207E-02 1,midg,midg; igrid,midg,midg -1.0610778E-02 3.2840170E-02 gauss-seidel spectral radius is 0.9985224 estimated iterations to convergence 206 setup time was (sec) 0.8200000 now iterating at: 03:40:15 rms-change max change #iterations 4.166249 164.9502 at 10iterations 1.887867 69.45602 at 20iterations 0.8576024 27.67520 at 30iterations 0.3908550 12.77121 at 40iterations 0.1776132 5.652224 at 50iterations 8.1040613E-02 2.558907 at 60iterations 3.7046861E-02 1.286636 at 70iterations 1.6834700E-02 0.5113306 at 80iterations 7.6296660E-03 0.2497535 at 90iterations 3.4920701E-03 0.1146255 at 100iterations 1.5848341E-03 4.9535751E-02 at 110iterations 7.2348071E-04 2.3500443E-02 at 120iterations finished qdiffx linear iterations at : 03:40:21 total time elapsed so far: 6.940000 # loops : 120 mean,max change (kT/e) : 7.2348071E-04 2.3500443E-02 energy calculations done at 6.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.130000 DelPhi exited at 03:40:22 7.130u 0.191s 0:07.99 91.6% 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 Tue Oct 11 2011 at 03:40:22 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3185 !!! WARNING: HIZ 79 has a net charge of 0.2000 !!! WARNING: GLU 288 has a net charge of -2.0000 !!! WARNING: ZN3 300 has a net charge of 1.4000 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.718572 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): -11.14500 36.88800 ymin,ymax (A): -27.30600 21.40400 zmin,zma (A): -13.40700 45.52100 x,y,z range (A): 48.03300 48.71000 58.92800 scale (grids/A): 2.718572 object centre (A): 12.87150 -2.951000 16.05700 number of atom coordinates read : 3185 total number of charged atoms : 2769 net assigned charge : -1.759978 assigned positive charge : 443.5083 centred at (gu) : 89.60995 93.98373 100.8544 assigned negative charge : -445.2691 centred at (gu) : 88.67568 93.81794 100.3023 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 176343 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24049 grid for indexing accessible points = 1.400000 m= 89914 mr = 130283 m= 30613 mr = 74503 m= 6227 mr = 24631 m= 697 mr = 4444 m= 39 mr = 431 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 10478 time to turn everything in is 1.310000 number of dielectric boundary points 69527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 22149 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) : 1.812381 object centre at (A) : 12.87150 -2.951000 16.05700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.048796 0.2410901 midg,1,midg; midg,igrid,midg -6.0668074E-02 -0.2708487 1,midg,midg; igrid,midg,midg -9.4461814E-02 0.3306432 gauss-seidel spectral radius is 0.9992265 estimated iterations to convergence 284 setup time was (sec) 1.610000 now iterating at: 03:40:24 rms-change max change #iterations 9.932207 315.3642 at 10iterations 5.730479 143.2567 at 20iterations 3.291609 68.85149 at 30iterations 1.884159 37.33842 at 40iterations 1.076805 21.75936 at 50iterations 0.6151334 13.27028 at 60iterations 0.3504461 6.239487 at 70iterations 0.1999944 3.460125 at 80iterations 0.1137852 2.298096 at 90iterations 6.4848348E-02 1.119633 at 100iterations 3.6855232E-02 0.6630173 at 110iterations 2.0966230E-02 0.3896103 at 120iterations 1.1934817E-02 0.2165279 at 130iterations 6.7812665E-03 0.1218910 at 140iterations 3.8697126E-03 7.8725815E-02 at 150iterations 2.2071302E-03 3.8473129E-02 at 160iterations 1.2624434E-03 2.3302317E-02 at 170iterations 7.2668202E-04 1.4082909E-02 at 180iterations finished qdiffx linear iterations at : 03:40:34 total time elapsed so far: 11.37000 # loops : 180 mean,max change (kT/e) : 7.2668202E-04 1.4082909E-02 energy calculations done at 11.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.54000 DelPhi exited at 03:40:35 11.544u 0.235s 0:12.75 92.3% 0+0k 0+0io 0pf+0w