Mon Oct 10 14:08:05 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 14:08:05 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2728 !!! WARNING: MG3 365 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5065525 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): 22.16600 78.16600 ymin,ymax (A): -10.92100 59.35800 zmin,zma (A): 3.195000 54.98600 x,y,z range (A): 56.00000 70.27900 51.79100 scale (grids/A): 0.5065525 object centre (A): 50.16600 24.21850 29.09050 number of atom coordinates read : 2728 total number of charged atoms : 2593 net assigned charge : 2.400012 assigned positive charge : 398.5737 centred at (gu) : 89.79442 87.33877 90.05199 assigned negative charge : -396.1742 centred at (gu) : 89.72665 87.25265 89.98055 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 4517 nv = 96 ne = 84 npr = 54611 no. pairs analyzed = 54611 no. exposed pairs = 3537 no. arc points = 25608 no. surface atoms = 1195 nbur = 1533 mkacc time = 0.1200000 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 = 1.680000 m= 150 mr = 2132 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2584 ## 437 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6033 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4063046E-11 1.1773667E-10 midg,1,midg; midg,igrid,midg -1.5283508E-10 6.6243948E-11 1,midg,midg; igrid,midg,midg -5.3306803E-11 1.0584351E-10 gauss-seidel spectral radius is 0.9799308 estimated iterations to convergence 58 setup time was (sec) 0.5600000 now iterating at: 14:08:06 rms-change max change #iterations 4.6454027E-02 9.770497 at 10iterations 2.5802900E-03 0.5461502 at 20iterations 1.3532401E-04 2.2050858E-02 at 30iterations 7.4251025E-06 1.5792847E-03 at 40iterations 4.3328149E-07 8.6784363E-05 at 50iterations finished qdiffx linear iterations at : 14:08:09 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 4.3328149E-07 8.6784363E-05 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 14:08:09 3.379u 0.181s 0:04.01 88.5% 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 14:08:09 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2728 !!! WARNING: MG3 365 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.519657 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): 22.16600 78.16600 ymin,ymax (A): -10.92100 59.35800 zmin,zma (A): 3.195000 54.98600 x,y,z range (A): 56.00000 70.27900 51.79100 scale (grids/A): 1.519657 object centre (A): 50.16600 24.21850 29.09050 number of atom coordinates read : 2728 total number of charged atoms : 2593 net assigned charge : 2.400012 assigned positive charge : 398.5737 centred at (gu) : 89.38279 82.01558 90.15524 assigned negative charge : -396.1742 centred at (gu) : 89.17963 81.75746 89.94125 start vw surface at 0.2300000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 50945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25608 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 13607 mr = 32954 m= 1069 mr = 8548 m= 12 mr = 372 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 113 time to turn everything in is 0.5000000 number of dielectric boundary points 23759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 345 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19457 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) : 0.5065525 object centre at (A) : 50.16600 24.21850 29.09050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1891262E-03 1.7283780E-03 midg,1,midg; midg,igrid,midg 5.4235840E-03 1.7365793E-02 1,midg,midg; igrid,midg,midg -7.9223365E-03 3.5292641E-03 gauss-seidel spectral radius is 0.9978531 estimated iterations to convergence 172 setup time was (sec) 0.7800000 now iterating at: 14:08:10 rms-change max change #iterations 2.672060 143.0725 at 10iterations 1.020087 53.81750 at 20iterations 0.3935973 16.49388 at 30iterations 0.1522280 6.625988 at 40iterations 5.8718096E-02 2.697365 at 50iterations 2.2598477E-02 0.9135027 at 60iterations 8.7217791E-03 0.4110947 at 70iterations 3.3640768E-03 0.1300869 at 80iterations 1.2984897E-03 5.3905964E-02 at 90iterations 5.0021539E-04 2.3625135E-02 at 100iterations 1.9423451E-04 1.0755539E-02 at 110iterations 7.4622942E-05 3.4661293E-03 at 120iterations finished qdiffx linear iterations at : 14:08:17 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 7.4622942E-05 3.4661293E-03 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 14:08:17 7.523u 0.187s 0:08.12 94.8% 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 14:08:18 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2728 !!! WARNING: MG3 365 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.279486 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): 22.16600 78.16600 ymin,ymax (A): -10.92100 59.35800 zmin,zma (A): 3.195000 54.98600 x,y,z range (A): 56.00000 70.27900 51.79100 scale (grids/A): 2.279486 object centre (A): 50.16600 24.21850 29.09050 number of atom coordinates read : 2728 total number of charged atoms : 2593 net assigned charge : 2.400012 assigned positive charge : 398.5737 centred at (gu) : 89.07396 78.02317 90.23267 assigned negative charge : -396.1742 centred at (gu) : 88.76939 77.63615 89.91170 start vw surface at 0.1800000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 118458 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25608 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 49385 mr = 81113 m= 11521 mr = 37466 m= 1411 mr = 7901 m= 65 mr = 720 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 411 time to turn everything in is 0.9600000 number of dielectric boundary points 53629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 48 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 20687 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) : 1.519657 object centre at (A) : 50.16600 24.21850 29.09050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4818959E-02 1.9360507E-02 midg,1,midg; midg,igrid,midg 0.1062491 0.3657669 1,midg,midg; igrid,midg,midg -0.1804006 5.8942109E-02 gauss-seidel spectral radius is 0.9990118 estimated iterations to convergence 252 setup time was (sec) 1.290000 now iterating at: 14:08:19 rms-change max change #iterations 7.134734 316.3503 at 10iterations 3.837345 101.4280 at 20iterations 2.045177 54.57043 at 30iterations 1.087595 29.92327 at 40iterations 0.5774600 15.72124 at 50iterations 0.3047680 7.774924 at 60iterations 0.1610209 4.231159 at 70iterations 8.4657751E-02 2.246382 at 80iterations 4.4759005E-02 1.032440 at 90iterations 2.3525501E-02 0.5850277 at 100iterations 1.2378152E-02 0.3501387 at 110iterations 6.5085879E-03 0.1578789 at 120iterations 3.4258137E-03 8.4577560E-02 at 130iterations 1.7947539E-03 4.1986465E-02 at 140iterations 9.4451616E-04 2.2511482E-02 at 150iterations 4.9570296E-04 1.1218429E-02 at 160iterations 2.6078057E-04 6.4015388E-03 at 170iterations 1.3722069E-04 3.2229424E-03 at 180iterations finished qdiffx linear iterations at : 14:08:30 total time elapsed so far: 11.99000 # loops : 180 mean,max change (kT/e) : 1.3722069E-04 3.2229424E-03 energy calculations done at 11.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 14:08:31 12.180u 0.278s 0:13.22 94.1% 0+0k 0+0io 0pf+0w