Sun Oct 9 07:10:10 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 Sun Oct 9 2011 at 07:10:11 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 !!! WARNING: NAP 191 has a net charge of -2.0000 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: 0.6746129 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): -13.08900 38.67300 ymin,ymax (A): -22.42100 29.23900 zmin,zma (A): -15.43000 37.34100 x,y,z range (A): 51.76200 51.66000 52.77100 scale (grids/A): 0.6746129 object centre (A): 12.79200 3.409000 10.95550 number of atom coordinates read : 2004 total number of charged atoms : 1867 net assigned charge : 1.000008 assigned positive charge : 299.1051 centred at (gu) : 90.47668 90.42970 89.82317 assigned negative charge : -298.1052 centred at (gu) : 90.63251 90.36006 89.69226 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6257 nv = 96 ne = 84 npr = 41725 no. pairs analyzed = 41725 no. exposed pairs = 2470 no. arc points = 18049 no. surface atoms = 835 nbur = 1169 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 369 mr = 3409 m= 4 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2500000 number of dielectric boundary points 3165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1694 ## 140 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7063 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6078199E-08 3.1116755E-08 midg,1,midg; midg,igrid,midg -1.0417682E-08 2.0895476E-08 1,midg,midg; igrid,midg,midg 3.4053887E-08 -3.3999154E-08 gauss-seidel spectral radius is 0.9885568 estimated iterations to convergence 76 setup time was (sec) 0.4900000 now iterating at: 07:10:11 rms-change max change #iterations 0.1636152 26.17100 at 10iterations 1.7948829E-02 2.748293 at 20iterations 2.0060716E-03 0.2818642 at 30iterations 2.2395470E-04 3.4572601E-02 at 40iterations 2.4709892E-05 3.6849976E-03 at 50iterations finished qdiffx linear iterations at : 07:10:14 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 2.4709892E-05 3.6849976E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 07:10:14 3.299u 0.196s 0:03.76 92.5% 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 Sun Oct 9 2011 at 07:10:14 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 !!! WARNING: NAP 191 has a net charge of -2.0000 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: 2.023839 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): -13.08900 38.67300 ymin,ymax (A): -22.42100 29.23900 zmin,zma (A): -15.43000 37.34100 x,y,z range (A): 51.76200 51.66000 52.77100 scale (grids/A): 2.023839 object centre (A): 12.79200 3.409000 10.95550 number of atom coordinates read : 2004 total number of charged atoms : 1867 net assigned charge : 1.000008 assigned positive charge : 299.1051 centred at (gu) : 91.43007 91.28912 89.46945 assigned negative charge : -298.1052 centred at (gu) : 91.89790 91.08035 89.07690 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66394 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18049 grid for indexing accessible points = 1.400000 m= 24985 mr = 45590 m= 3873 mr = 18523 m= 271 mr = 2369 m= 5 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1693 time to turn everything in is 0.5000000 number of dielectric boundary points 28935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 82 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 14781 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) : 0.6746129 object centre at (A) : 12.79200 3.409000 10.95550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4059267E-02 1.5353909E-02 midg,1,midg; midg,igrid,midg 1.7602824E-02 4.5075838E-02 1,midg,midg; igrid,midg,midg 1.6689407E-02 -4.5857422E-02 gauss-seidel spectral radius is 0.9987310 estimated iterations to convergence 222 setup time was (sec) 0.8000000 now iterating at: 07:10:15 rms-change max change #iterations 4.190716 188.0746 at 10iterations 2.013432 72.89708 at 20iterations 0.9668037 31.09825 at 30iterations 0.4653099 16.04348 at 40iterations 0.2234847 7.284096 at 50iterations 0.1076902 3.621925 at 60iterations 5.1636927E-02 1.643561 at 70iterations 2.4938406E-02 0.7951546 at 80iterations 1.1936160E-02 0.3750381 at 90iterations 5.7720789E-03 0.1948347 at 100iterations 2.7707017E-03 9.3634605E-02 at 110iterations 1.3316398E-03 4.2716980E-02 at 120iterations finished qdiffx linear iterations at : 07:10:22 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 1.3316398E-03 4.2716980E-02 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.480000 DelPhi exited at 07:10:22 7.481u 0.239s 0:08.06 95.6% 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 Sun Oct 9 2011 at 07:10:22 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 !!! WARNING: NAP 191 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.035758 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): -13.08900 38.67300 ymin,ymax (A): -22.42100 29.23900 zmin,zma (A): -15.43000 37.34100 x,y,z range (A): 51.76200 51.66000 52.77100 scale (grids/A): 3.035758 object centre (A): 12.79200 3.409000 10.95550 number of atom coordinates read : 2004 total number of charged atoms : 1867 net assigned charge : 1.000008 assigned positive charge : 299.1051 centred at (gu) : 92.14518 91.93366 89.20419 assigned negative charge : -298.1052 centred at (gu) : 92.84680 91.62058 88.61538 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 152716 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18049 grid for indexing accessible points = 1.400000 m= 79290 mr = 109344 m= 29750 mr = 65449 m= 7014 mr = 23939 m= 1063 mr = 5094 m= 90 mr = 699 m= 3 mr = 56 m= 0 mr = 3 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 5423 time to turn everything in is 1.240000 number of dielectric boundary points 65342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 14935 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) : 2.023839 object centre at (A) : 12.79200 3.409000 10.95550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6538952 0.1204954 midg,1,midg; midg,igrid,midg 0.2689939 0.4520516 1,midg,midg; igrid,midg,midg 0.2872332 -0.3595608 gauss-seidel spectral radius is 0.9992751 estimated iterations to convergence 293 setup time was (sec) 1.550000 now iterating at: 07:10:24 rms-change max change #iterations 9.489895 392.9413 at 10iterations 5.477365 127.4350 at 20iterations 3.169487 64.33097 at 30iterations 1.835229 35.12119 at 40iterations 1.059132 19.88253 at 50iterations 0.6108988 12.60834 at 60iterations 0.3536332 8.059420 at 70iterations 0.2039760 3.941216 at 80iterations 0.1175704 1.996334 at 90iterations 6.7756794E-02 1.299103 at 100iterations 3.9102789E-02 0.7230530 at 110iterations 2.2571370E-02 0.4332218 at 120iterations 1.3014750E-02 0.2486343 at 130iterations 7.5271730E-03 0.1417542 at 140iterations 4.3488271E-03 9.2599869E-02 at 150iterations 2.5002055E-03 4.6947479E-02 at 160iterations 1.4412178E-03 2.7456284E-02 at 170iterations 8.3254423E-04 1.4664650E-02 at 180iterations finished qdiffx linear iterations at : 07:10:35 total time elapsed so far: 11.93000 # loops : 180 mean,max change (kT/e) : 8.3254423E-04 1.4664650E-02 energy calculations done at 11.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.10000 DelPhi exited at 07:10:35 12.101u 0.254s 0:12.67 97.4% 0+0k 0+0io 0pf+0w