Sat Oct 8 11:34:57 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 Sat Oct 8 2011 at 11:34:57 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4268 !!! WARNING: HIR 440 has a net charge of 0.5140 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: 0.5279158 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): -1.511000 65.92400 ymin,ymax (A): -10.34500 37.87900 zmin,zma (A): -19.25900 43.99500 x,y,z range (A): 67.43500 48.22400 63.25400 scale (grids/A): 0.5279158 object centre (A): 32.20650 13.76700 12.36800 number of atom coordinates read : 4268 total number of charged atoms : 4102 net assigned charge : -8.485952 assigned positive charge : 640.7473 centred at (gu) : 87.69096 89.84580 90.32970 assigned negative charge : -649.2355 centred at (gu) : 87.74729 89.92785 90.36838 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6894 nv = 96 ne = 84 npr = 95090 no. pairs analyzed = 95090 no. exposed pairs = 4405 no. arc points = 30037 no. surface atoms = 1506 nbur = 2762 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 = 1.624000 m= 214 mr = 3885 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 84 time to turn everything in is 0.4200000 number of dielectric boundary points 3219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3061 ## 392 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9621 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9721499E-11 -4.8475801E-10 midg,1,midg; midg,igrid,midg 1.3549015E-10 -6.3176681E-10 1,midg,midg; igrid,midg,midg 2.8546982E-11 -2.9803052E-10 gauss-seidel spectral radius is 0.9815828 estimated iterations to convergence 61 setup time was (sec) 0.6500000 now iterating at: 11:34:59 rms-change max change #iterations 7.4434899E-02 11.24900 at 10iterations 4.9835932E-03 0.7860374 at 20iterations 5.3940254E-04 9.3805313E-02 at 30iterations 9.3092407E-05 1.7951965E-02 at 40iterations 1.9095296E-05 3.6773682E-03 at 50iterations finished qdiffx linear iterations at : 11:35:04 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.9095296E-05 3.6773682E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 11:35:05 3.477u 0.169s 0:07.64 47.5% 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 Sat Oct 8 2011 at 11:35:05 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4268 !!! WARNING: HIR 440 has a net charge of 0.5140 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: 1.583747 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): -1.511000 65.92400 ymin,ymax (A): -10.34500 37.87900 zmin,zma (A): -19.25900 43.99500 x,y,z range (A): 67.43500 48.22400 63.25400 scale (grids/A): 1.583747 object centre (A): 32.20650 13.76700 12.36800 number of atom coordinates read : 4268 total number of charged atoms : 4102 net assigned charge : -8.485952 assigned positive charge : 640.7473 centred at (gu) : 83.07191 89.53646 90.98807 assigned negative charge : -649.2355 centred at (gu) : 83.24152 89.78317 91.10462 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 78774 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30037 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21224 mr = 56767 m= 1834 mr = 14486 m= 36 mr = 900 m= 0 mr = 4 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 5126 time to turn everything in is 0.5700000 number of dielectric boundary points 29711 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 377 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 31247 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) : 0.5279158 object centre at (A) : 32.20650 13.76700 12.36800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3452751E-02 -1.2724079E-02 midg,1,midg; midg,igrid,midg -5.1145367E-03 -1.2489868E-02 1,midg,midg; igrid,midg,midg 2.0454425E-02 -6.8402155E-03 gauss-seidel spectral radius is 0.9981535 estimated iterations to convergence 185 setup time was (sec) 0.8700000 now iterating at: 11:35:06 rms-change max change #iterations 3.801697 149.8475 at 10iterations 1.571783 55.85909 at 20iterations 0.6528866 25.39085 at 30iterations 0.2702663 8.452530 at 40iterations 0.1122038 3.489569 at 50iterations 4.6701379E-02 1.419289 at 60iterations 1.9452963E-02 0.7004642 at 70iterations 8.1216730E-03 0.2692947 at 80iterations 3.3900200E-03 0.1180692 at 90iterations 1.4220877E-03 4.8294067E-02 at 100iterations 6.0387747E-04 2.2087097E-02 at 110iterations 2.5926862E-04 8.7738037E-03 at 120iterations finished qdiffx linear iterations at : 11:35:14 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 2.5926862E-04 8.7738037E-03 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.420000 DelPhi exited at 11:35:14 8.424u 0.226s 0:09.36 92.3% 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 8 2011 at 11:35:14 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4268 !!! WARNING: HIR 440 has a net charge of 0.5140 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: 2.375621 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): -1.511000 65.92400 ymin,ymax (A): -10.34500 37.87900 zmin,zma (A): -19.25900 43.99500 x,y,z range (A): 67.43500 48.22400 63.25400 scale (grids/A): 2.375621 object centre (A): 32.20650 13.76700 12.36800 number of atom coordinates read : 4268 total number of charged atoms : 4102 net assigned charge : -8.485952 assigned positive charge : 640.7473 centred at (gu) : 79.60773 89.30424 91.48185 assigned negative charge : -649.2355 centred at (gu) : 79.86203 89.67478 91.65696 start vw surface at 0.1900000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 184636 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30037 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 77840 mr = 139428 m= 19000 mr = 61969 m= 2804 mr = 14073 m= 142 mr = 1838 m= 0 mr = 44 time to grow re-entrant surface = 0.7400001 no. cavity mid-points inaccessible to solvent = 17742 time to turn everything in is 1.350000 number of dielectric boundary points 67070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 32740 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) : 1.583747 object centre at (A) : 32.20650 13.76700 12.36800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3098612 -0.2470642 midg,1,midg; midg,igrid,midg -9.9556565E-02 -0.1832833 1,midg,midg; igrid,midg,midg 0.5927377 -0.3544456 gauss-seidel spectral radius is 0.9991406 estimated iterations to convergence 269 setup time was (sec) 1.670000 now iterating at: 11:35:16 rms-change max change #iterations 9.885799 394.2340 at 10iterations 5.516051 134.9982 at 20iterations 3.074265 61.20670 at 30iterations 1.710850 35.25948 at 40iterations 0.9470363 17.78028 at 50iterations 0.5233216 9.856842 at 60iterations 0.2890839 5.834480 at 70iterations 0.1598520 3.012063 at 80iterations 8.8124067E-02 1.610147 at 90iterations 4.8575595E-02 0.8671913 at 100iterations 2.6766470E-02 0.4778099 at 110iterations 1.4749594E-02 0.2799025 at 120iterations 8.1403023E-03 0.1544037 at 130iterations 4.4914521E-03 8.0531120E-02 at 140iterations 2.4776384E-03 4.4879913E-02 at 150iterations 1.3696336E-03 2.9434204E-02 at 160iterations 7.5876992E-04 1.4445066E-02 at 170iterations 4.2213817E-04 8.0070496E-03 at 180iterations finished qdiffx linear iterations at : 11:35:26 total time elapsed so far: 12.02000 # loops : 180 mean,max change (kT/e) : 4.2213817E-04 8.0070496E-03 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 11:35:27 12.206u 0.193s 0:12.86 96.3% 0+0k 0+0io 0pf+0w