Sat Oct 15 14:22:12 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 Sat Oct 15 2011 at 14:22:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3451 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6428894 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): 12.12500 62.85800 ymin,ymax (A): -41.24000 10.33900 zmin,zma (A): 30.66900 86.04400 x,y,z range (A): 50.73300 51.57900 55.37500 scale (grids/A): 0.6428894 object centre (A): 37.49150 -15.45050 58.35650 number of atom coordinates read : 3451 total number of charged atoms : 3303 net assigned charge : 3.000040 assigned positive charge : 529.5694 centred at (gu) : 89.40562 90.85578 89.24240 assigned negative charge : -526.5706 centred at (gu) : 89.42934 90.81654 89.31229 start vw surface at 0.1900000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 9402 nv = 96 ne = 84 npr = 71539 no. pairs analyzed = 71539 no. exposed pairs = 3869 no. arc points = 26577 no. surface atoms = 1301 nbur = 2150 mkacc time = 0.2400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 510 mr = 5564 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 48 time to turn everything in is 0.5100000 number of dielectric boundary points 4290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2615 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 11447 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9311537E-08 -6.3238943E-09 midg,1,midg; midg,igrid,midg -1.7794454E-09 1.3480672E-08 1,midg,midg; igrid,midg,midg 9.7464863E-09 4.5316337E-10 gauss-seidel spectral radius is 0.9875273 estimated iterations to convergence 73 setup time was (sec) 0.8700000 now iterating at: 14:22:13 rms-change max change #iterations 0.1752899 22.24134 at 10iterations 1.8196560E-02 2.289424 at 20iterations 2.2287967E-03 0.2653694 at 30iterations 6.2945863E-04 9.0696335E-02 at 40iterations 2.8775007E-04 4.0029526E-02 at 50iterations finished qdiffx linear iterations at : 14:22:17 total time elapsed so far: 4.860000 # loops : 50 mean,max change (kT/e) : 2.8775007E-04 4.0029526E-02 energy calculations done at 4.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.080000 DelPhi exited at 14:22:18 5.086u 0.428s 0:05.83 94.3% 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 Sat Oct 15 2011 at 14:22:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3451 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.928668 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): 12.12500 62.85800 ymin,ymax (A): -41.24000 10.33900 zmin,zma (A): 30.66900 86.04400 x,y,z range (A): 50.73300 51.57900 55.37500 scale (grids/A): 1.928668 object centre (A): 37.49150 -15.45050 58.35650 number of atom coordinates read : 3451 total number of charged atoms : 3303 net assigned charge : 3.000040 assigned positive charge : 529.5694 centred at (gu) : 88.21597 92.56623 87.72642 assigned negative charge : -526.5706 centred at (gu) : 88.28757 92.44934 87.93651 start vw surface at 0.1800000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 101550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26577 grid for indexing accessible points = 1.400000 m= 39865 mr = 74079 m= 6821 mr = 30454 m= 442 mr = 4368 m= 8 mr = 156 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 1854 time to turn everything in is 1.050000 number of dielectric boundary points 39629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 195 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 26067 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) : 0.6428894 object centre at (A) : 37.49150 -15.45050 58.35650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9656136E-02 -5.2568060E-03 midg,1,midg; midg,igrid,midg -7.0987586E-03 2.6572207E-02 1,midg,midg; igrid,midg,midg 1.5448680E-02 4.3565210E-02 gauss-seidel spectral radius is 0.9987346 estimated iterations to convergence 223 setup time was (sec) 1.420000 now iterating at: 14:22:20 rms-change max change #iterations 5.169410 207.6122 at 10iterations 2.499914 67.43738 at 20iterations 1.213513 33.12491 at 30iterations 0.5860164 16.83463 at 40iterations 0.2837702 8.198466 at 50iterations 0.1373049 3.743622 at 60iterations 6.6550545E-02 2.081703 at 70iterations 3.2270689E-02 0.9422054 at 80iterations 1.5710743E-02 0.4277878 at 90iterations 7.7259531E-03 0.2381439 at 100iterations 3.8742062E-03 0.1181946 at 110iterations 2.0402935E-03 5.2970886E-02 at 120iterations finished qdiffx linear iterations at : 14:22:30 total time elapsed so far: 11.94000 # loops : 120 mean,max change (kT/e) : 2.0402935E-03 5.2970886E-02 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.17000 DelPhi exited at 14:22:31 12.171u 0.502s 0:13.06 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 Sat Oct 15 2011 at 14:22:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3451 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.893002 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): 12.12500 62.85800 ymin,ymax (A): -41.24000 10.33900 zmin,zma (A): 30.66900 86.04400 x,y,z range (A): 50.73300 51.57900 55.37500 scale (grids/A): 2.893002 object centre (A): 37.49150 -15.45050 58.35650 number of atom coordinates read : 3451 total number of charged atoms : 3303 net assigned charge : 3.000040 assigned positive charge : 529.5694 centred at (gu) : 87.32381 93.84901 86.58964 assigned negative charge : -526.5706 centred at (gu) : 87.43120 93.67384 86.90479 start vw surface at 0.2000000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 234539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26577 grid for indexing accessible points = 1.400000 m= 127059 mr = 178197 m= 49059 mr = 106398 m= 12705 mr = 40206 m= 1924 mr = 9689 m= 125 mr = 1236 m= 0 mr = 59 time to grow re-entrant surface = 1.750000 no. cavity mid-points inaccessible to solvent = 6194 time to turn everything in is 2.810000 number of dielectric boundary points 89626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.990000 number of grid points assigned charge 26424 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) : 1.928668 object centre at (A) : 37.49150 -15.45050 58.35650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3991937 0.1947662 midg,1,midg; midg,igrid,midg -5.6429859E-02 0.3124163 1,midg,midg; igrid,midg,midg 0.2242840 0.5477620 gauss-seidel spectral radius is 0.9992932 estimated iterations to convergence 297 setup time was (sec) 3.210000 now iterating at: 14:22:35 rms-change max change #iterations 11.98710 516.4204 at 10iterations 7.161853 146.5163 at 20iterations 4.259685 100.0765 at 30iterations 2.516222 47.51987 at 40iterations 1.487926 27.02285 at 50iterations 0.8755639 15.50115 at 60iterations 0.5146797 8.717644 at 70iterations 0.3015899 5.102482 at 80iterations 0.1769541 3.064379 at 90iterations 0.1038808 1.784826 at 100iterations 6.0781229E-02 1.004997 at 110iterations 3.5575334E-02 0.5678062 at 120iterations 2.0819290E-02 0.3236637 at 130iterations 1.2183411E-02 0.1856394 at 140iterations 7.1447464E-03 0.1110115 at 150iterations 4.1927081E-03 6.5979004E-02 at 160iterations 2.4802370E-03 4.2286873E-02 at 170iterations 1.4861773E-03 2.4452209E-02 at 180iterations finished qdiffx linear iterations at : 14:22:53 total time elapsed so far: 21.29000 # loops : 180 mean,max change (kT/e) : 1.4861773E-03 2.4452209E-02 energy calculations done at 21.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.50000 DelPhi exited at 14:22:53 21.502u 0.520s 0:22.36 98.4% 0+0k 0+0io 0pf+0w