Mon Oct 10 20:15:51 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 20:15:51 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2532 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: 0.6187968 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): -10.48000 45.43200 ymin,ymax (A): -16.93200 36.23800 zmin,zma (A): -12.05000 45.48100 x,y,z range (A): 55.91200 53.17000 57.53100 scale (grids/A): 0.6187968 object centre (A): 17.47600 9.653000 16.71550 number of atom coordinates read : 2532 total number of charged atoms : 2395 net assigned charge : -3.999990 assigned positive charge : 373.6650 centred at (gu) : 89.20980 90.53022 90.39845 assigned negative charge : -377.6659 centred at (gu) : 89.13688 90.63533 90.29842 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6662 nv = 96 ne = 84 npr = 49958 no. pairs analyzed = 49958 no. exposed pairs = 3585 no. arc points = 25552 no. surface atoms = 1186 nbur = 1346 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 380 mr = 3274 m= 6 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2497 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8020 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5683345E-09 3.4422698E-09 midg,1,midg; midg,igrid,midg 3.0393297E-09 -1.0889623E-08 1,midg,midg; igrid,midg,midg -9.0888701E-09 1.2100809E-09 gauss-seidel spectral radius is 0.9864861 estimated iterations to convergence 70 setup time was (sec) 0.3700000 now iterating at: 20:15:52 rms-change max change #iterations 0.1205868 19.01955 at 10iterations 1.1116205E-02 1.637054 at 20iterations 1.0009892E-03 0.1644230 at 30iterations 9.0700356E-05 1.3599396E-02 at 40iterations 8.5408255E-06 1.4801025E-03 at 50iterations finished qdiffx linear iterations at : 20:15:55 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 8.5408255E-06 1.4801025E-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) 3.350000 DelPhi exited at 20:15:55 3.350u 0.170s 0:04.29 82.0% 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 20:15:56 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2532 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: 1.856390 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): -10.48000 45.43200 ymin,ymax (A): -16.93200 36.23800 zmin,zma (A): -12.05000 45.48100 x,y,z range (A): 55.91200 53.17000 57.53100 scale (grids/A): 1.856390 object centre (A): 17.47600 9.653000 16.71550 number of atom coordinates read : 2532 total number of charged atoms : 2395 net assigned charge : -3.999990 assigned positive charge : 373.6650 centred at (gu) : 87.62901 91.59022 91.19488 assigned negative charge : -377.6659 centred at (gu) : 87.41057 91.90608 90.89509 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71575 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25552 grid for indexing accessible points = 1.400000 m= 24841 mr = 46522 m= 3780 mr = 17164 m= 216 mr = 2055 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 34622 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18776 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) : 0.6187968 object centre at (A) : 17.47600 9.653000 16.71550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2489486E-02 -1.8102147E-02 midg,1,midg; midg,igrid,midg 1.4310719E-02 -2.8275883E-02 1,midg,midg; igrid,midg,midg -5.5872300E-03 5.6738156E-04 gauss-seidel spectral radius is 0.9985836 estimated iterations to convergence 211 setup time was (sec) 0.5800000 now iterating at: 20:15:56 rms-change max change #iterations 4.005987 191.3278 at 10iterations 1.832763 74.32446 at 20iterations 0.8437325 29.10733 at 30iterations 0.3896931 13.29257 at 40iterations 0.1793475 6.090174 at 50iterations 8.2399920E-02 3.011789 at 60iterations 3.7959341E-02 1.422930 at 70iterations 1.7534319E-02 0.5856915 at 80iterations 8.1037031E-03 0.2871113 at 90iterations 3.7293914E-03 0.1179347 at 100iterations 1.7225202E-03 6.0993195E-02 at 110iterations 7.9386198E-04 2.9273987E-02 at 120iterations finished qdiffx linear iterations at : 20:16:03 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 7.9386198E-04 2.9273987E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 20:16:04 7.746u 0.186s 0:08.69 91.1% 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 Mon Oct 10 2011 at 20:16:04 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2532 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: 2.784586 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): -10.48000 45.43200 ymin,ymax (A): -16.93200 36.23800 zmin,zma (A): -12.05000 45.48100 x,y,z range (A): 55.91200 53.17000 57.53100 scale (grids/A): 2.784586 object centre (A): 17.47600 9.653000 16.71550 number of atom coordinates read : 2532 total number of charged atoms : 2395 net assigned charge : -3.999990 assigned positive charge : 373.6650 centred at (gu) : 86.44347 92.38522 91.79218 assigned negative charge : -377.6659 centred at (gu) : 86.11589 92.85919 91.34275 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 165587 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25552 grid for indexing accessible points = 1.400000 m= 79072 mr = 113863 m= 28659 mr = 61961 m= 6620 mr = 21833 m= 788 mr = 4429 m= 31 mr = 474 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 78192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 19160 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) : 1.856390 object centre at (A) : 17.47600 9.653000 16.71550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1623167 -0.1654460 midg,1,midg; midg,igrid,midg 0.1936539 -0.2229559 1,midg,midg; igrid,midg,midg 0.1198052 -5.9091374E-03 gauss-seidel spectral radius is 0.9992574 estimated iterations to convergence 290 setup time was (sec) 1.170000 now iterating at: 20:16:06 rms-change max change #iterations 9.718101 302.2322 at 10iterations 5.772132 176.6238 at 20iterations 3.386440 82.08600 at 30iterations 1.985630 46.09061 at 40iterations 1.152339 29.84237 at 50iterations 0.6678979 15.66846 at 60iterations 0.3861777 7.805254 at 70iterations 0.2226781 4.996613 at 80iterations 0.1279424 2.536533 at 90iterations 7.3735826E-02 1.390491 at 100iterations 4.2407431E-02 0.8225632 at 110iterations 2.4346234E-02 0.5298790 at 120iterations 1.3957371E-02 0.2627182 at 130iterations 8.0396542E-03 0.1650238 at 140iterations 4.6230443E-03 8.9618683E-02 at 150iterations 2.6510200E-03 5.7520032E-02 at 160iterations 1.5217855E-03 2.8434753E-02 at 170iterations 8.7585958E-04 1.7970562E-02 at 180iterations finished qdiffx linear iterations at : 20:16:17 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 8.7585958E-04 1.7970562E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 20:16:18 12.707u 0.218s 0:13.30 97.0% 0+0k 0+0io 0pf+0w