Tue Oct 11 06:55:39 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 Tue Oct 11 2011 at 06:55:39 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 = 2859 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: 0.5582475 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): -18.48000 45.29100 ymin,ymax (A): 21.48800 78.71800 zmin,zma (A): -72.17300 -23.75100 x,y,z range (A): 63.77100 57.23000 48.42200 scale (grids/A): 0.5582475 object centre (A): 13.40550 50.10300 -47.96200 number of atom coordinates read : 2859 total number of charged atoms : 2721 net assigned charge : 1.500005 assigned positive charge : 414.3517 centred at (gu) : 89.42546 89.72800 89.80692 assigned negative charge : -412.8523 centred at (gu) : 89.46195 89.77797 89.77993 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5790 nv = 96 ne = 84 npr = 58183 no. pairs analyzed = 58183 no. exposed pairs = 3697 no. arc points = 25661 no. surface atoms = 1260 nbur = 1599 mkacc time = 0.1700000 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 = 1.540000 m= 312 mr = 2955 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2549 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7453 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2139098E-10 3.8799666E-10 midg,1,midg; midg,igrid,midg 6.6981143E-10 -3.1729031E-10 1,midg,midg; igrid,midg,midg 5.7277871E-10 -1.7975900E-10 gauss-seidel spectral radius is 0.9834443 estimated iterations to convergence 64 setup time was (sec) 0.6300000 now iterating at: 06:55:40 rms-change max change #iterations 7.9503074E-02 14.06996 at 10iterations 5.6158993E-03 0.9264240 at 20iterations 4.2810262E-04 6.4885139E-02 at 30iterations 5.2023184E-05 1.0246277E-02 at 40iterations 1.2138940E-05 2.6335716E-03 at 50iterations finished qdiffx linear iterations at : 06:55:43 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 1.2138940E-05 2.6335716E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 06:55:44 4.090u 0.274s 0:05.06 86.1% 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 Tue Oct 11 2011 at 06:55:44 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 = 2859 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: 1.674742 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): -18.48000 45.29100 ymin,ymax (A): 21.48800 78.71800 zmin,zma (A): -72.17300 -23.75100 x,y,z range (A): 63.77100 57.23000 48.42200 scale (grids/A): 1.674742 object centre (A): 13.40550 50.10300 -47.96200 number of atom coordinates read : 2859 total number of charged atoms : 2721 net assigned charge : 1.500005 assigned positive charge : 414.3517 centred at (gu) : 88.27613 89.18345 89.41985 assigned negative charge : -412.8523 centred at (gu) : 88.38563 89.33372 89.33921 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 63373 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25661 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 21455 mr = 42183 m= 2838 mr = 15135 m= 100 mr = 1636 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 28793 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 187 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20943 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) : 0.5582475 object centre at (A) : 13.40550 50.10300 -47.96200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6261414E-03 1.0608039E-02 midg,1,midg; midg,igrid,midg -5.0591994E-03 1.1787216E-02 1,midg,midg; igrid,midg,midg 5.8067399E-03 -1.8088508E-02 gauss-seidel spectral radius is 0.9982736 estimated iterations to convergence 191 setup time was (sec) 0.9000000 now iterating at: 06:55:45 rms-change max change #iterations 3.361126 176.9081 at 10iterations 1.425286 63.04398 at 20iterations 0.6087151 23.49360 at 30iterations 0.2585999 10.34102 at 40iterations 0.1104759 3.835251 at 50iterations 4.6978842E-02 1.778120 at 60iterations 2.0018980E-02 0.7231779 at 70iterations 8.5266437E-03 0.3551502 at 80iterations 3.6396126E-03 0.1268983 at 90iterations 1.5500082E-03 5.4609478E-02 at 100iterations 6.6195207E-04 2.2802353E-02 at 110iterations 2.8441093E-04 1.0118484E-02 at 120iterations finished qdiffx linear iterations at : 06:55:53 total time elapsed so far: 9.100000 # loops : 120 mean,max change (kT/e) : 2.8441093E-04 1.0118484E-02 energy calculations done at 9.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.280000 DelPhi exited at 06:55:54 9.284u 0.290s 0:10.04 95.3% 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 Tue Oct 11 2011 at 06:55:54 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 = 2859 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: 2.512114 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): -18.48000 45.29100 ymin,ymax (A): 21.48800 78.71800 zmin,zma (A): -72.17300 -23.75100 x,y,z range (A): 63.77100 57.23000 48.42200 scale (grids/A): 2.512114 object centre (A): 13.40550 50.10300 -47.96200 number of atom coordinates read : 2859 total number of charged atoms : 2721 net assigned charge : 1.500005 assigned positive charge : 414.3517 centred at (gu) : 87.41400 88.77496 89.12963 assigned negative charge : -412.8523 centred at (gu) : 87.57822 89.00045 89.00884 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 146713 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25661 grid for indexing accessible points = 1.400000 m= 70599 mr = 103177 m= 23918 mr = 55887 m= 4959 mr = 18778 m= 448 mr = 3642 m= 5 mr = 229 m= 0 mr = 2 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.450000 number of dielectric boundary points 64927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 21755 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) : 1.674742 object centre at (A) : 13.40550 50.10300 -47.96200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8050002E-02 0.1888947 midg,1,midg; midg,igrid,midg -8.0130070E-02 0.1906426 1,midg,midg; igrid,midg,midg 4.0284403E-02 -0.4907311 gauss-seidel spectral radius is 0.9991696 estimated iterations to convergence 274 setup time was (sec) 1.760000 now iterating at: 06:55:56 rms-change max change #iterations 8.631976 300.1524 at 10iterations 4.909013 132.4781 at 20iterations 2.775784 61.97841 at 30iterations 1.562347 35.25109 at 40iterations 0.8787618 17.81222 at 50iterations 0.4904316 10.44970 at 60iterations 0.2746080 5.586926 at 70iterations 0.1531461 3.076685 at 80iterations 8.5084431E-02 1.783972 at 90iterations 4.7525030E-02 1.017105 at 100iterations 2.6448488E-02 0.5586252 at 110iterations 1.4653435E-02 0.2843571 at 120iterations 8.1482939E-03 0.1749649 at 130iterations 4.5395149E-03 8.4365845E-02 at 140iterations 2.5173556E-03 4.8525810E-02 at 150iterations 1.3975750E-03 3.0838013E-02 at 160iterations 7.7699759E-04 1.4480591E-02 at 170iterations 4.3116638E-04 8.2607269E-03 at 180iterations finished qdiffx linear iterations at : 06:56:09 total time elapsed so far: 15.12000 # loops : 180 mean,max change (kT/e) : 4.3116638E-04 8.2607269E-03 energy calculations done at 15.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.29000 DelPhi exited at 06:56:10 15.288u 0.325s 0:16.10 96.8% 0+0k 0+0io 0pf+0w