Mon Oct 10 22:01:46 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 22:01:46 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 = 2893 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: 0.5535687 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): -24.98500 31.79400 ymin,ymax (A): -33.84100 22.97600 zmin,zma (A): -6.946000 57.36400 x,y,z range (A): 56.77900 56.81700 64.31000 scale (grids/A): 0.5535687 object centre (A): 3.404499 -5.432500 25.20900 number of atom coordinates read : 2893 total number of charged atoms : 2799 net assigned charge : 2.500007 assigned positive charge : 427.2771 centred at (gu) : 89.88665 89.14588 91.00250 assigned negative charge : -424.7785 centred at (gu) : 89.73681 89.22952 90.93217 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5921 nv = 96 ne = 84 npr = 56548 no. pairs analyzed = 56548 no. exposed pairs = 3994 no. arc points = 28460 no. surface atoms = 1341 nbur = 1552 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 = 1.568000 m= 223 mr = 2813 m= 0 mr = 6 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2979 ## 390 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7821 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0813754E-10 1.0032279E-09 midg,1,midg; midg,igrid,midg 1.1026130E-09 -4.1204257E-10 1,midg,midg; igrid,midg,midg -1.1144152E-09 1.3929090E-09 gauss-seidel spectral radius is 0.9831781 estimated iterations to convergence 63 setup time was (sec) 0.5800000 now iterating at: 22:01:47 rms-change max change #iterations 7.3266059E-02 14.01512 at 10iterations 5.1796371E-03 0.9391260 at 20iterations 4.0677498E-04 6.6291809E-02 at 30iterations 5.0104125E-05 6.8283081E-03 at 40iterations 9.7006905E-06 1.2197495E-03 at 50iterations finished qdiffx linear iterations at : 22:01:51 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 9.7006905E-06 1.2197495E-03 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 22:01:52 4.491u 0.397s 0:05.70 85.6% 0+0k 0+0io 6pf+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 22:01:52 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 = 2893 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.660706 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): -24.98500 31.79400 ymin,ymax (A): -33.84100 22.97600 zmin,zma (A): -6.946000 57.36400 x,y,z range (A): 56.77900 56.81700 64.31000 scale (grids/A): 1.660706 object centre (A): 3.404499 -5.432500 25.20900 number of atom coordinates read : 2893 total number of charged atoms : 2799 net assigned charge : 2.500007 assigned positive charge : 427.2771 centred at (gu) : 89.65923 87.43707 93.00634 assigned negative charge : -424.7785 centred at (gu) : 89.21040 87.68833 92.79630 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 65384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28460 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19615 mr = 42440 m= 2165 mr = 12785 m= 65 mr = 965 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 226 time to turn everything in is 0.5400000 number of dielectric boundary points 31035 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 304 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21546 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) : 0.5535687 object centre at (A) : 3.404499 -5.432500 25.20900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4000826E-03 5.5085225E-03 midg,1,midg; midg,igrid,midg 1.3462518E-03 -1.0127819E-02 1,midg,midg; igrid,midg,midg -1.1403341E-02 2.0263376E-02 gauss-seidel spectral radius is 0.9982570 estimated iterations to convergence 190 setup time was (sec) 0.8500000 now iterating at: 22:01:53 rms-change max change #iterations 3.323139 214.9658 at 10iterations 1.401211 59.91431 at 20iterations 0.5955868 27.40564 at 30iterations 0.2505948 10.62218 at 40iterations 0.1063983 3.638455 at 50iterations 4.5187362E-02 1.576650 at 60iterations 1.9163724E-02 0.7845650 at 70iterations 8.1213554E-03 0.2764359 at 80iterations 3.4410385E-03 0.1229630 at 90iterations 1.4644974E-03 5.2619934E-02 at 100iterations 6.2433706E-04 2.2239685E-02 at 110iterations 2.6713574E-04 9.7274780E-03 at 120iterations finished qdiffx linear iterations at : 22:02:04 total time elapsed so far: 11.32000 # loops : 120 mean,max change (kT/e) : 2.6713574E-04 9.7274780E-03 energy calculations done at 11.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.49000 DelPhi exited at 22:02:04 11.494u 0.448s 0:12.27 97.2% 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 22:02:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2893 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: 2.491059 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): -24.98500 31.79400 ymin,ymax (A): -33.84100 22.97600 zmin,zma (A): -6.946000 57.36400 x,y,z range (A): 56.77900 56.81700 64.31000 scale (grids/A): 2.491059 object centre (A): 3.404499 -5.432500 25.20900 number of atom coordinates read : 2893 total number of charged atoms : 2799 net assigned charge : 2.500007 assigned positive charge : 427.2771 centred at (gu) : 89.48864 86.15537 94.50946 assigned negative charge : -424.7785 centred at (gu) : 88.81557 86.53246 94.19455 start vw surface at 0.1200000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 151724 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28460 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67208 mr = 104536 m= 19433 mr = 51399 m= 3254 mr = 13937 m= 228 mr = 2009 m= 4 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 750 time to turn everything in is 1.390000 number of dielectric boundary points 69889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 22373 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) : 1.660706 object centre at (A) : 3.404499 -5.432500 25.20900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2143513 0.1911384 midg,1,midg; midg,igrid,midg -5.0683129E-03 -0.1270180 1,midg,midg; igrid,midg,midg -0.2799011 0.2736339 gauss-seidel spectral radius is 0.9991687 estimated iterations to convergence 274 setup time was (sec) 1.720000 now iterating at: 22:02:06 rms-change max change #iterations 8.700548 319.1139 at 10iterations 4.945500 122.6533 at 20iterations 2.805613 67.52702 at 30iterations 1.581279 37.92467 at 40iterations 0.8908669 19.71357 at 50iterations 0.4989060 10.39625 at 60iterations 0.2779418 6.212016 at 70iterations 0.1551490 3.494343 at 80iterations 8.6628504E-02 1.822042 at 90iterations 4.8100028E-02 1.084333 at 100iterations 2.6778113E-02 0.5439186 at 110iterations 1.4896898E-02 0.3259478 at 120iterations 8.2850466E-03 0.1964083 at 130iterations 4.5995652E-03 9.1078758E-02 at 140iterations 2.5568637E-03 5.5077553E-02 at 150iterations 1.4210079E-03 3.1509399E-02 at 160iterations 7.9032098E-04 1.6713142E-02 at 170iterations 4.3828218E-04 8.5649490E-03 at 180iterations finished qdiffx linear iterations at : 22:02:22 total time elapsed so far: 17.50000 # loops : 180 mean,max change (kT/e) : 4.3828218E-04 8.5649490E-03 energy calculations done at 17.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.67000 DelPhi exited at 22:02:23 17.675u 0.469s 0:18.77 96.5% 0+0k 0+0io 0pf+0w