Sat Oct 15 13:14:05 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+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 15 2011 at 13:14:05 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3893 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5628904 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): 3.496000 66.71301 ymin,ymax (A): 0.7010001 61.84400 zmin,zma (A): -0.7909999 62.45400 x,y,z range (A): 63.21701 61.14300 63.24500 scale (grids/A): 0.5628904 object centre (A): 35.10450 31.27250 30.83150 number of atom coordinates read : 3893 total number of charged atoms : 3744 net assigned charge : 0.6210319 assigned positive charge : 588.1008 centred at (gu) : 89.37695 88.23283 88.09682 assigned negative charge : -587.4826 centred at (gu) : 89.34589 88.35156 88.01685 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8244 nv = 96 ne = 84 npr = 76076 no. pairs analyzed = 76076 no. exposed pairs = 5168 no. arc points = 35315 no. surface atoms = 1742 nbur = 2151 mkacc time = 0.1800000 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= 413 mr = 4313 m= 3 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 4322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3506 ## 345 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10558 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9758697E-09 8.4702972E-10 midg,1,midg; midg,igrid,midg 3.0159877E-09 -1.2169608E-09 1,midg,midg; igrid,midg,midg -5.0628041E-10 4.8595811E-10 gauss-seidel spectral radius is 0.9837947 estimated iterations to convergence 65 setup time was (sec) 0.6500000 now iterating at: 13:14:06 rms-change max change #iterations 0.1001301 16.08031 at 10iterations 7.8330617E-03 1.084389 at 20iterations 1.9084716E-03 0.2473869 at 30iterations 1.1606427E-03 0.1312027 at 40iterations 7.3816610E-04 8.3423615E-02 at 50iterations finished qdiffx linear iterations at : 13:14:09 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 7.3816610E-04 8.3423615E-02 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 13:14:09 3.573u 0.154s 0:04.03 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 15 2011 at 13:14:09 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3893 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.688671 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): 3.496000 66.71301 ymin,ymax (A): 0.7010001 61.84400 zmin,zma (A): -0.7909999 62.45400 x,y,z range (A): 63.21701 61.14300 63.24500 scale (grids/A): 1.688671 object centre (A): 35.10450 31.27250 30.83150 number of atom coordinates read : 3893 total number of charged atoms : 3744 net assigned charge : 0.6210319 assigned positive charge : 588.1008 centred at (gu) : 88.12955 84.69712 84.28929 assigned negative charge : -587.4826 centred at (gu) : 88.03721 85.05422 84.05000 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 91005 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35315 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30852 mr = 62588 m= 4003 mr = 21250 m= 139 mr = 2105 m= 0 mr = 23 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 160 time to turn everything in is 0.6800000 number of dielectric boundary points 40033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 340 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 28901 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) : 0.5628904 object centre at (A) : 35.10450 31.27250 30.83150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9645137E-02 -9.7530736E-03 midg,1,midg; midg,igrid,midg 2.5985327E-02 -2.1098631E-03 1,midg,midg; igrid,midg,midg 6.5283803E-03 2.6433903E-03 gauss-seidel spectral radius is 0.9984019 estimated iterations to convergence 198 setup time was (sec) 0.9700000 now iterating at: 13:14:10 rms-change max change #iterations 4.219920 177.4693 at 10iterations 1.851898 67.99104 at 20iterations 0.8210611 25.02402 at 30iterations 0.3622085 11.92764 at 40iterations 0.1593531 6.116756 at 50iterations 7.0627421E-02 2.172411 at 60iterations 3.1444646E-02 1.011846 at 70iterations 1.4063659E-02 0.4399496 at 80iterations 6.4967186E-03 0.2216759 at 90iterations 3.2774729E-03 0.1039369 at 100iterations 1.9903516E-03 6.1080933E-02 at 110iterations 1.4648194E-03 3.9525986E-02 at 120iterations finished qdiffx linear iterations at : 13:14:17 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 1.4648194E-03 3.9525986E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 13:14:18 7.952u 0.197s 0:08.50 95.7% 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 15 2011 at 13:14:18 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3893 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.533006 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): 3.496000 66.71301 ymin,ymax (A): 0.7010001 61.84400 zmin,zma (A): -0.7909999 62.45400 x,y,z range (A): 63.21701 61.14300 63.24500 scale (grids/A): 2.533006 object centre (A): 35.10450 31.27250 30.83150 number of atom coordinates read : 3893 total number of charged atoms : 3744 net assigned charge : 0.6210319 assigned positive charge : 588.1008 centred at (gu) : 87.19394 82.04532 81.43368 assigned negative charge : -587.4826 centred at (gu) : 87.05579 82.58121 81.07500 start vw surface at 0.1900000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 211095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35315 grid for indexing accessible points = 1.400000 m= 103118 mr = 153021 m= 33313 mr = 81545 m= 6650 mr = 24957 m= 611 mr = 4451 m= 12 mr = 299 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 594 time to turn everything in is 1.690000 number of dielectric boundary points 90526 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 29931 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) : 1.688671 object centre at (A) : 35.10450 31.27250 30.83150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7300315 -0.1633672 midg,1,midg; midg,igrid,midg 0.3521689 -6.9055721E-02 1,midg,midg; igrid,midg,midg 0.1508227 -4.2909663E-02 gauss-seidel spectral radius is 0.9992340 estimated iterations to convergence 285 setup time was (sec) 2.010000 now iterating at: 13:14:20 rms-change max change #iterations 10.98013 425.1564 at 10iterations 6.540331 179.3085 at 20iterations 3.843930 79.04644 at 30iterations 2.244375 51.93460 at 40iterations 1.307282 28.14048 at 50iterations 0.7565675 14.53421 at 60iterations 0.4368833 8.115623 at 70iterations 0.2518931 5.768792 at 80iterations 0.1447466 2.743124 at 90iterations 8.3053835E-02 1.534203 at 100iterations 4.7698323E-02 0.8810234 at 110iterations 2.7363738E-02 0.4655685 at 120iterations 1.5686605E-02 0.2931480 at 130iterations 9.0257162E-03 0.1699371 at 140iterations 5.1948619E-03 9.0076447E-02 at 150iterations 3.0380685E-03 6.4880371E-02 at 160iterations 1.8234694E-03 3.2638550E-02 at 170iterations 1.1565671E-03 2.2237778E-02 at 180iterations finished qdiffx linear iterations at : 13:14:31 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 1.1565671E-03 2.2237778E-02 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 13:14:31 13.101u 0.214s 0:13.67 97.3% 0+0k 0+0io 0pf+0w