Sat Oct 8 11:36:09 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 8 2011 at 11:36:10 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 = 4359 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: 0.5646133 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): 60.22700 115.7910 ymin,ymax (A): 20.30600 82.95600 zmin,zma (A): -7.673000 55.37900 x,y,z range (A): 55.56400 62.65000 63.05200 scale (grids/A): 0.5646133 object centre (A): 88.00900 51.63100 23.85300 number of atom coordinates read : 4359 total number of charged atoms : 4214 net assigned charge : -0.9999489 assigned positive charge : 655.1882 centred at (gu) : 89.51646 90.18885 89.72565 assigned negative charge : -656.1914 centred at (gu) : 89.70803 90.13460 89.54060 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8936 nv = 96 ne = 84 npr = 91122 no. pairs analyzed = 91122 no. exposed pairs = 4945 no. arc points = 33385 no. surface atoms = 1672 nbur = 2687 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 = 1.512000 m= 386 mr = 5208 m= 0 mr = 27 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 83 time to turn everything in is 0.3000000 number of dielectric boundary points 4087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3526 ## 433 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 11810 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0371737E-09 3.1369498E-09 midg,1,midg; midg,igrid,midg -1.1285270E-09 9.5113672E-10 1,midg,midg; igrid,midg,midg 3.9115680E-09 -3.4726668E-09 gauss-seidel spectral radius is 0.9839158 estimated iterations to convergence 65 setup time was (sec) 0.5200000 now iterating at: 11:36:10 rms-change max change #iterations 0.1060176 14.74507 at 10iterations 8.2629947E-03 1.126538 at 20iterations 9.6833974E-04 0.1183653 at 30iterations 2.4635319E-04 3.0427694E-02 at 40iterations 8.3335537E-05 1.0920525E-02 at 50iterations finished qdiffx linear iterations at : 11:36:14 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 8.3335537E-05 1.0920525E-02 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.890000 DelPhi exited at 11:36:14 3.897u 0.237s 0:04.52 91.1% 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 Sat Oct 8 2011 at 11:36:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4359 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: 1.693840 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): 60.22700 115.7910 ymin,ymax (A): 20.30600 82.95600 zmin,zma (A): -7.673000 55.37900 x,y,z range (A): 55.56400 62.65000 63.05200 scale (grids/A): 1.693840 object centre (A): 88.00900 51.63100 23.85300 number of atom coordinates read : 4359 total number of charged atoms : 4214 net assigned charge : -0.9999489 assigned positive charge : 655.1882 centred at (gu) : 88.54773 90.56524 89.17593 assigned negative charge : -656.1914 centred at (gu) : 89.12360 90.40319 88.62136 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 99922 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33385 grid for indexing accessible points = 1.400000 m= 34385 mr = 72471 m= 4235 mr = 25561 m= 127 mr = 2522 m= 0 mr = 16 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 5893 time to turn everything in is 0.5000000 number of dielectric boundary points 38099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 351 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 32576 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) : 0.5646133 object centre at (A) : 88.00900 51.63100 23.85300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8188802E-02 2.7649831E-02 midg,1,midg; midg,igrid,midg -3.1616319E-02 3.5659876E-02 1,midg,midg; igrid,midg,midg 3.8898081E-02 -3.3193987E-02 gauss-seidel spectral radius is 0.9984459 estimated iterations to convergence 201 setup time was (sec) 0.7700000 now iterating at: 11:36:15 rms-change max change #iterations 4.470188 174.4724 at 10iterations 1.994273 61.31728 at 20iterations 0.8901061 30.02512 at 30iterations 0.3957122 12.73859 at 40iterations 0.1767946 5.971210 at 50iterations 7.8623667E-02 2.128223 at 60iterations 3.5254244E-02 1.076347 at 70iterations 1.5823709E-02 0.4681799 at 80iterations 7.0884712E-03 0.2128401 at 90iterations 3.2027527E-03 8.7989807E-02 at 100iterations 1.4718117E-03 3.9125443E-02 at 110iterations 6.9463666E-04 1.9920349E-02 at 120iterations finished qdiffx linear iterations at : 11:36:23 total time elapsed so far: 8.990000 # loops : 120 mean,max change (kT/e) : 6.9463666E-04 1.9920349E-02 energy calculations done at 8.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.120000 DelPhi exited at 11:36:24 9.124u 0.261s 0:09.69 96.8% 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 Sat Oct 8 2011 at 11:36:24 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 = 4359 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: 2.540760 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): 60.22700 115.7910 ymin,ymax (A): 20.30600 82.95600 zmin,zma (A): -7.673000 55.37900 x,y,z range (A): 55.56400 62.65000 63.05200 scale (grids/A): 2.540760 object centre (A): 88.00900 51.63100 23.85300 number of atom coordinates read : 4359 total number of charged atoms : 4214 net assigned charge : -0.9999489 assigned positive charge : 655.1882 centred at (gu) : 87.82123 90.84751 88.76356 assigned negative charge : -656.1914 centred at (gu) : 88.68525 90.60486 87.93188 start vw surface at 0.1100000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 231936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33385 grid for indexing accessible points = 1.400000 m= 116146 mr = 175732 m= 37087 mr = 95997 m= 7200 mr = 29740 m= 604 mr = 5308 m= 12 mr = 347 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 19518 time to turn everything in is 1.220000 number of dielectric boundary points 85861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 33687 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) : 1.693840 object centre at (A) : 88.00900 51.63100 23.85300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3612742 0.2680183 midg,1,midg; midg,igrid,midg -0.8009531 0.7200724 1,midg,midg; igrid,midg,midg 0.6581906 -0.4290545 gauss-seidel spectral radius is 0.9992372 estimated iterations to convergence 286 setup time was (sec) 1.490000 now iterating at: 11:36:26 rms-change max change #iterations 11.23182 324.1908 at 10iterations 6.554489 168.1361 at 20iterations 3.796253 88.30199 at 30iterations 2.193117 42.17789 at 40iterations 1.263613 22.09071 at 50iterations 0.7263576 14.79221 at 60iterations 0.4166538 7.255527 at 70iterations 0.2391579 3.961477 at 80iterations 0.1365865 2.430607 at 90iterations 7.8116998E-02 1.446555 at 100iterations 4.4714011E-02 0.8242106 at 110iterations 2.5561133E-02 0.3994331 at 120iterations 1.4655199E-02 0.2250988 at 130iterations 8.3602406E-03 0.1345367 at 140iterations 4.8072664E-03 8.7845802E-02 at 150iterations 2.7701652E-03 4.2982101E-02 at 160iterations 1.6102957E-03 2.7435303E-02 at 170iterations 9.5034525E-04 1.4999330E-02 at 180iterations finished qdiffx linear iterations at : 11:36:39 total time elapsed so far: 14.37000 # loops : 180 mean,max change (kT/e) : 9.5034525E-04 1.4999330E-02 energy calculations done at 14.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.51000 DelPhi exited at 11:36:39 14.510u 0.315s 0:15.25 97.1% 0+0k 0+0io 0pf+0w