Mon Oct 10 16:59:47 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 Mon Oct 10 2011 at 16:59:47 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4129 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5142279 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): -15.11800 36.72100 ymin,ymax (A): -30.47000 31.56500 zmin,zma (A): -4.123000 65.10700 x,y,z range (A): 51.83900 62.03500 69.23000 scale (grids/A): 0.5142279 object centre (A): 10.80150 0.5474997 30.49200 number of atom coordinates read : 4129 total number of charged atoms : 3887 net assigned charge : 3.300024 assigned positive charge : 610.1967 centred at (gu) : 90.34961 90.80458 87.06681 assigned negative charge : -606.9001 centred at (gu) : 90.20377 90.85445 87.06767 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6837 nv = 96 ne = 84 npr = 84790 no. pairs analyzed = 84790 no. exposed pairs = 5326 no. arc points = 37244 no. surface atoms = 1780 nbur = 2349 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 237 mr = 3440 m= 0 mr = 8 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3535 ## 530 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 9114 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2058349E-10 2.5053605E-11 midg,1,midg; midg,igrid,midg 1.4591385E-10 -9.1443908E-11 1,midg,midg; igrid,midg,midg -2.9442668E-10 4.5785192E-10 gauss-seidel spectral radius is 0.9806125 estimated iterations to convergence 59 setup time was (sec) 0.4800000 now iterating at: 16:59:47 rms-change max change #iterations 6.6648044E-02 14.09064 at 10iterations 3.6688887E-03 0.6290665 at 20iterations 2.5760671E-04 3.6346436E-02 at 30iterations 4.7519963E-05 6.7205429E-03 at 40iterations 1.5237642E-05 2.1941662E-03 at 50iterations finished qdiffx linear iterations at : 16:59:50 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.5237642E-05 2.1941662E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 16:59:51 3.540u 0.174s 0:04.27 86.8% 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 16:59:51 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4129 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.542684 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): -15.11800 36.72100 ymin,ymax (A): -30.47000 31.56500 zmin,zma (A): -4.123000 65.10700 x,y,z range (A): 51.83900 62.03500 69.23000 scale (grids/A): 1.542684 object centre (A): 10.80150 0.5474997 30.49200 number of atom coordinates read : 4129 total number of charged atoms : 3887 net assigned charge : 3.300024 assigned positive charge : 610.1967 centred at (gu) : 91.04768 92.41239 81.19920 assigned negative charge : -606.9001 centred at (gu) : 90.61086 92.56321 81.20289 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 77103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37244 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 21944 mr = 51879 m= 1913 mr = 14344 m= 52 mr = 797 m= 0 mr = 1 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.3900000 number of dielectric boundary points 33991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 462 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 29261 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) : 0.5142279 object centre at (A) : 10.80150 0.5474997 30.49200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4429034E-03 7.1241870E-03 midg,1,midg; midg,igrid,midg -2.7956904E-04 -1.0092186E-02 1,midg,midg; igrid,midg,midg -2.4458021E-03 9.9547543E-03 gauss-seidel spectral radius is 0.9980778 estimated iterations to convergence 181 setup time was (sec) 0.6100000 now iterating at: 16:59:52 rms-change max change #iterations 3.497578 157.3390 at 10iterations 1.414737 49.86494 at 20iterations 0.5759878 18.89635 at 30iterations 0.2339040 10.23592 at 40iterations 9.4933905E-02 3.492636 at 50iterations 3.8696319E-02 1.263252 at 60iterations 1.5668400E-02 0.5416374 at 70iterations 6.4176517E-03 0.2048378 at 80iterations 2.6030890E-03 8.6741775E-02 at 90iterations 1.0653599E-03 3.8866043E-02 at 100iterations 4.3313799E-04 1.4968872E-02 at 110iterations 1.7796604E-04 6.3544214E-03 at 120iterations finished qdiffx linear iterations at : 16:59:59 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 1.7796604E-04 6.3544214E-03 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 17:00:00 7.908u 0.214s 0:08.81 92.0% 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 17:00:00 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4129 !!! WARNING: HEM 818 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.314026 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): -15.11800 36.72100 ymin,ymax (A): -30.47000 31.56500 zmin,zma (A): -4.123000 65.10700 x,y,z range (A): 51.83900 62.03500 69.23000 scale (grids/A): 2.314026 object centre (A): 10.80150 0.5474997 30.49200 number of atom coordinates read : 4129 total number of charged atoms : 3887 net assigned charge : 3.300024 assigned positive charge : 610.1967 centred at (gu) : 91.57124 93.61817 76.79847 assigned negative charge : -606.9001 centred at (gu) : 90.91627 93.84464 76.80424 start vw surface at 0.1200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 179649 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37244 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 78277 mr = 127711 m= 19533 mr = 60355 m= 2807 mr = 13799 m= 144 mr = 1714 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 271 time to turn everything in is 0.9300000 number of dielectric boundary points 76801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 31024 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) : 1.542684 object centre at (A) : 10.80150 0.5474997 30.49200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1353032 0.2288788 midg,1,midg; midg,igrid,midg -6.2662140E-02 -0.2530190 1,midg,midg; igrid,midg,midg -2.1689901E-02 0.1502732 gauss-seidel spectral radius is 0.9991367 estimated iterations to convergence 269 setup time was (sec) 1.170000 now iterating at: 17:00:01 rms-change max change #iterations 9.486012 326.9172 at 10iterations 5.376641 133.1750 at 20iterations 3.023492 75.10176 at 30iterations 1.695607 41.34283 at 40iterations 0.9495448 20.67198 at 50iterations 0.5279713 13.14085 at 60iterations 0.2940241 7.557614 at 70iterations 0.1624205 3.905024 at 80iterations 8.9962095E-02 2.038733 at 90iterations 4.9704060E-02 1.014874 at 100iterations 2.7442180E-02 0.6219202 at 110iterations 1.5155986E-02 0.3234863 at 120iterations 8.3550839E-03 0.1867168 at 130iterations 4.6031261E-03 9.1449976E-02 at 140iterations 2.5336228E-03 5.4363251E-02 at 150iterations 1.3987202E-03 2.9309273E-02 at 160iterations 7.7065802E-04 1.6141891E-02 at 170iterations 4.2419252E-04 8.6743832E-03 at 180iterations finished qdiffx linear iterations at : 17:00:13 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 4.2419252E-04 8.6743832E-03 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 17:00:13 12.814u 0.237s 0:13.43 97.0% 0+0k 0+0io 0pf+0w