Sun Oct 9 18:11:39 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 Sun Oct 9 2011 at 18:11:39 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5001 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5468258 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): 3.202000 68.30500 ymin,ymax (A): -9.213000 53.47600 zmin,zma (A): -2.660000 61.64500 x,y,z range (A): 65.10300 62.68900 64.30499 scale (grids/A): 0.5468258 object centre (A): 35.75350 22.13150 29.49250 number of atom coordinates read : 5001 total number of charged atoms : 4857 net assigned charge : -0.8789496 assigned positive charge : 766.7159 centred at (gu) : 87.54958 89.38875 89.55955 assigned negative charge : -767.6005 centred at (gu) : 87.43013 89.41399 89.56490 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 9842 nv = 96 ne = 84 npr = 100516 no. pairs analyzed = 100516 no. exposed pairs = 5949 no. arc points = 40420 no. surface atoms = 2031 nbur = 2970 mkacc time = 0.2200000 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 = 1.568000 m= 436 mr = 5556 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 4700 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4109 ## 472 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 12864 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9042742E-11 -7.3797787E-11 midg,1,midg; midg,igrid,midg 3.2252864E-10 -2.7179028E-10 1,midg,midg; igrid,midg,midg -2.6945057E-09 7.4155732E-10 gauss-seidel spectral radius is 0.9829050 estimated iterations to convergence 63 setup time was (sec) 0.6900000 now iterating at: 18:11:40 rms-change max change #iterations 0.1001530 12.94644 at 10iterations 9.4630299E-03 1.464783 at 20iterations 2.9006910E-03 0.3396759 at 30iterations 1.3235385E-03 0.1517553 at 40iterations 6.2767701E-04 7.7935219E-02 at 50iterations finished qdiffx linear iterations at : 18:11:43 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 6.2767701E-04 7.7935219E-02 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 18:11:43 3.247u 0.134s 0:03.74 90.1% 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 Sun Oct 9 2011 at 18:11:43 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5001 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.640477 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): 3.202000 68.30500 ymin,ymax (A): -9.213000 53.47600 zmin,zma (A): -2.660000 61.64500 x,y,z range (A): 65.10300 62.68900 64.30499 scale (grids/A): 1.640477 object centre (A): 35.75350 22.13150 29.49250 number of atom coordinates read : 5001 total number of charged atoms : 4857 net assigned charge : -0.8789496 assigned positive charge : 766.7159 centred at (gu) : 82.64716 88.16514 88.67729 assigned negative charge : -767.6005 centred at (gu) : 82.29032 88.24178 88.69463 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 109770 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40420 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 37907 mr = 79272 m= 4392 mr = 27228 m= 150 mr = 2280 m= 3 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 43423 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 412 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 37283 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) : 0.5468258 object centre at (A) : 35.75350 22.13150 29.49250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6406978E-02 -2.6338035E-02 midg,1,midg; midg,igrid,midg 1.7202562E-02 6.6356193E-03 1,midg,midg; igrid,midg,midg -2.5728323E-02 1.9743159E-02 gauss-seidel spectral radius is 0.9983900 estimated iterations to convergence 198 setup time was (sec) 1.000000 now iterating at: 18:11:44 rms-change max change #iterations 4.677437 168.6142 at 10iterations 2.053820 72.41330 at 20iterations 0.9014419 24.63934 at 30iterations 0.3968462 12.45638 at 40iterations 0.1754344 5.254921 at 50iterations 7.7268027E-02 2.076574 at 60iterations 3.4622256E-02 0.9672604 at 70iterations 1.5884846E-02 0.5209389 at 80iterations 7.8529166E-03 0.2574539 at 90iterations 4.3840599E-03 0.1178589 at 100iterations 2.8203158E-03 7.8029513E-02 at 110iterations 2.0083201E-03 4.9842834E-02 at 120iterations finished qdiffx linear iterations at : 18:11:50 total time elapsed so far: 7.060000 # loops : 120 mean,max change (kT/e) : 2.0083201E-03 4.9842834E-02 energy calculations done at 7.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.230000 DelPhi exited at 18:11:51 7.233u 0.156s 0:07.71 95.7% 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 Sun Oct 9 2011 at 18:11:51 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5001 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.460716 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): 3.202000 68.30500 ymin,ymax (A): -9.213000 53.47600 zmin,zma (A): -2.660000 61.64500 x,y,z range (A): 65.10300 62.68900 64.30499 scale (grids/A): 2.460716 object centre (A): 35.75350 22.13150 29.49250 number of atom coordinates read : 5001 total number of charged atoms : 4857 net assigned charge : -0.8789496 assigned positive charge : 766.7159 centred at (gu) : 78.97041 87.24706 88.01563 assigned negative charge : -767.6005 centred at (gu) : 78.43547 87.36265 88.04202 start vw surface at 0.2100000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 255162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40420 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 128408 mr = 193201 m= 40012 mr = 104210 m= 6971 mr = 30764 m= 534 mr = 4670 m= 8 mr = 266 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.880000 number of dielectric boundary points 97984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 38825 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) : 1.640477 object centre at (A) : 35.75350 22.13150 29.49250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3082204 -0.5557992 midg,1,midg; midg,igrid,midg 0.1196236 -6.7372710E-02 1,midg,midg; igrid,midg,midg -0.5068915 0.3159646 gauss-seidel spectral radius is 0.9992394 estimated iterations to convergence 286 setup time was (sec) 2.180000 now iterating at: 18:11:53 rms-change max change #iterations 11.96268 306.2079 at 10iterations 7.040205 142.2068 at 20iterations 4.121990 88.47256 at 30iterations 2.398216 42.76825 at 40iterations 1.388332 26.12785 at 50iterations 0.8024638 14.55801 at 60iterations 0.4625872 8.806210 at 70iterations 0.2661066 4.531914 at 80iterations 0.1529614 2.549221 at 90iterations 8.7951832E-02 1.601267 at 100iterations 5.0754741E-02 0.8649063 at 110iterations 2.9418640E-02 0.5316486 at 120iterations 1.7377388E-02 0.3375092 at 130iterations 1.0529922E-02 0.1980267 at 140iterations 6.7091300E-03 0.1225131 at 150iterations 4.5845513E-03 8.5484505E-02 at 160iterations 3.3698473E-03 6.0045004E-02 at 170iterations 2.6312580E-03 4.5661926E-02 at 180iterations finished qdiffx linear iterations at : 18:12:03 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 2.6312580E-03 4.5661926E-02 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 18:12:04 12.233u 0.196s 0:12.72 97.6% 0+0k 0+0io 0pf+0w