Tue Oct 11 07:36:54 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 Tue Oct 11 2011 at 07:36:54 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2599 !!! WARNING: SEP 202 has a net charge of -0.4750 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: 0.6960330 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): -13.25700 37.89000 ymin,ymax (A): -21.70800 26.56500 zmin,zma (A): -5.713000 40.19000 x,y,z range (A): 51.14700 48.27300 45.90300 scale (grids/A): 0.6960330 object centre (A): 12.31650 2.428500 17.23850 number of atom coordinates read : 2599 total number of charged atoms : 2275 net assigned charge : 6.025004 assigned positive charge : 363.1312 centred at (gu) : 90.95544 88.03925 89.50323 assigned negative charge : -357.1067 centred at (gu) : 91.03658 88.01412 89.68430 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7897 nv = 96 ne = 84 npr = 47662 no. pairs analyzed = 47662 no. exposed pairs = 2832 no. arc points = 19640 no. surface atoms = 964 nbur = 1635 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 551 mr = 4630 m= 4 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1735 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8844 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2808586E-07 -3.7270702E-08 midg,1,midg; midg,igrid,midg 4.0184919E-08 3.4119108E-08 1,midg,midg; igrid,midg,midg 6.1175605E-08 3.3158858E-09 gauss-seidel spectral radius is 0.9892738 estimated iterations to convergence 79 setup time was (sec) 0.7200000 now iterating at: 07:36:55 rms-change max change #iterations 0.2028418 27.46078 at 10iterations 2.4710899E-02 3.194759 at 20iterations 3.4509692E-03 0.4895096 at 30iterations 6.0841563E-04 8.0390930E-02 at 40iterations 1.3833257E-04 2.1553040E-02 at 50iterations finished qdiffx linear iterations at : 07:36:59 total time elapsed so far: 4.580000 # loops : 50 mean,max change (kT/e) : 1.3833257E-04 2.1553040E-02 energy calculations done at 4.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.810000 DelPhi exited at 07:37:00 4.817u 0.447s 0:05.85 89.7% 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 07:37:00 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2599 !!! WARNING: SEP 202 has a net charge of -0.4750 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: 2.088099 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): -13.25700 37.89000 ymin,ymax (A): -21.70800 26.56500 zmin,zma (A): -5.713000 40.19000 x,y,z range (A): 51.14700 48.27300 45.90300 scale (grids/A): 2.088099 object centre (A): 12.31650 2.428500 17.23850 number of atom coordinates read : 2599 total number of charged atoms : 2275 net assigned charge : 6.025004 assigned positive charge : 363.1312 centred at (gu) : 92.86605 84.11736 88.50930 assigned negative charge : -357.1067 centred at (gu) : 93.10950 84.04234 89.05279 start vw surface at 0.1500000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 83500 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19640 grid for indexing accessible points = 1.400000 m= 34451 mr = 59566 m= 6820 mr = 26720 m= 553 mr = 4616 m= 11 mr = 286 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 34147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 18063 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) : 0.6960330 object centre at (A) : 12.31650 2.428500 17.23850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3872358E-02 -1.4133304E-02 midg,1,midg; midg,igrid,midg 1.5312608E-02 2.6352670E-02 1,midg,midg; igrid,midg,midg 1.7703384E-02 1.7282100E-02 gauss-seidel spectral radius is 0.9988273 estimated iterations to convergence 231 setup time was (sec) 1.230000 now iterating at: 07:37:01 rms-change max change #iterations 4.833049 215.4763 at 10iterations 2.403520 75.39857 at 20iterations 1.188011 33.57724 at 30iterations 0.5902458 19.58137 at 40iterations 0.2930892 8.511482 at 50iterations 0.1458577 4.157166 at 60iterations 7.2448775E-02 2.288181 at 70iterations 3.6055624E-02 1.025911 at 80iterations 1.8052015E-02 0.5164795 at 90iterations 9.0053035E-03 0.2835159 at 100iterations 4.5337002E-03 0.1482544 at 110iterations 2.3172160E-03 7.2612762E-02 at 120iterations finished qdiffx linear iterations at : 07:37:12 total time elapsed so far: 11.41000 # loops : 120 mean,max change (kT/e) : 2.3172160E-03 7.2612762E-02 energy calculations done at 11.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 07:37:12 11.630u 0.492s 0:12.49 97.0% 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 Tue Oct 11 2011 at 07:37:12 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2599 !!! WARNING: SEP 202 has a net charge of -0.4750 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: 3.132149 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): -13.25700 37.89000 ymin,ymax (A): -21.70800 26.56500 zmin,zma (A): -5.713000 40.19000 x,y,z range (A): 51.14700 48.27300 45.90300 scale (grids/A): 3.132149 object centre (A): 12.31650 2.428500 17.23850 number of atom coordinates read : 2599 total number of charged atoms : 2275 net assigned charge : 6.025004 assigned positive charge : 363.1312 centred at (gu) : 94.29897 81.17588 87.76374 assigned negative charge : -357.1067 centred at (gu) : 94.66417 81.06340 88.57922 start vw surface at 0.1500000 fill in re-entrant regions at 1.090000 boundary points on vw surface= 192170 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19640 grid for indexing accessible points = 1.400000 m= 106285 mr = 142847 m= 44685 mr = 89464 m= 12989 mr = 37258 m= 2491 mr = 10228 m= 215 mr = 1837 m= 3 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 1.470000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.720000 number of dielectric boundary points 77087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.880000 number of grid points assigned charge 18200 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) : 2.088099 object centre at (A) : 12.31650 2.428500 17.23850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5329769 -0.1603446 midg,1,midg; midg,igrid,midg 0.1015648 0.1846860 1,midg,midg; igrid,midg,midg 5.0580902E-03 8.4265843E-03 gauss-seidel spectral radius is 0.9993034 estimated iterations to convergence 299 setup time was (sec) 3.110000 now iterating at: 07:37:16 rms-change max change #iterations 10.79467 452.4480 at 10iterations 6.350444 118.6428 at 20iterations 3.747222 71.64544 at 30iterations 2.198432 39.66201 at 40iterations 1.293051 22.27223 at 50iterations 0.7560197 13.72987 at 60iterations 0.4436615 7.159811 at 70iterations 0.2595944 4.291621 at 80iterations 0.1520905 2.586698 at 90iterations 8.9170724E-02 1.418196 at 100iterations 5.2450873E-02 0.8785744 at 110iterations 3.0870782E-02 0.5228539 at 120iterations 1.8357275E-02 0.3046761 at 130iterations 1.1025872E-02 0.2016983 at 140iterations 6.7469482E-03 0.1224804 at 150iterations 4.2657135E-03 7.5790405E-02 at 160iterations 2.8128834E-03 5.0575256E-02 at 170iterations 1.9421708E-03 3.6155701E-02 at 180iterations finished qdiffx linear iterations at : 07:37:33 total time elapsed so far: 19.90000 # loops : 180 mean,max change (kT/e) : 1.9421708E-03 3.6155701E-02 energy calculations done at 19.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.11000 DelPhi exited at 07:37:33 20.119u 0.512s 0:21.10 97.7% 0+0k 0+0io 0pf+0w