Mon Oct 10 18:46:49 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 Mon Oct 10 2011 at 18:46:49 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3919 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: 0.5346228 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): -42.76000 10.56500 ymin,ymax (A): -18.38400 33.75500 zmin,zma (A): -77.36500 -10.77600 x,y,z range (A): 53.32500 52.13900 66.58900 scale (grids/A): 0.5346228 object centre (A): -16.09750 7.685499 -44.07050 number of atom coordinates read : 3919 total number of charged atoms : 3777 net assigned charge : 7.000044 assigned positive charge : 601.5421 centred at (gu) : 89.56910 89.57633 89.93723 assigned negative charge : -594.5452 centred at (gu) : 89.54312 89.43489 89.98363 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7464 nv = 96 ne = 84 npr = 75595 no. pairs analyzed = 75595 no. exposed pairs = 5225 no. arc points = 36578 no. surface atoms = 1730 nbur = 2189 mkacc time = 0.1300000 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 = 1.568000 m= 283 mr = 3791 m= 0 mr = 4 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2600000 number of dielectric boundary points 3952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3665 ## 517 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 9749 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5645116E-10 1.3038378E-11 midg,1,midg; midg,igrid,midg -6.1268418E-10 9.7234165E-10 1,midg,midg; igrid,midg,midg 1.4570631E-10 3.8738293E-10 gauss-seidel spectral radius is 0.9820498 estimated iterations to convergence 62 setup time was (sec) 0.4500000 now iterating at: 18:46:50 rms-change max change #iterations 7.5721435E-02 12.65009 at 10iterations 5.1311781E-03 0.8544159 at 20iterations 6.4607710E-04 0.1275444 at 30iterations 1.8689795E-04 3.7857056E-02 at 40iterations 6.6240595E-05 1.2058258E-02 at 50iterations finished qdiffx linear iterations at : 18:46:53 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 6.6240595E-05 1.2058258E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 18:46:53 3.480u 0.175s 0:04.22 86.4% 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 Mon Oct 10 2011 at 18:46:54 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3919 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: 1.603869 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): -42.76000 10.56500 ymin,ymax (A): -18.38400 33.75500 zmin,zma (A): -77.36500 -10.77600 x,y,z range (A): 53.32500 52.13900 66.58900 scale (grids/A): 1.603869 object centre (A): -16.09750 7.685499 -44.07050 number of atom coordinates read : 3919 total number of charged atoms : 3777 net assigned charge : 7.000044 assigned positive charge : 601.5421 centred at (gu) : 88.70596 88.72789 89.81087 assigned negative charge : -594.5452 centred at (gu) : 88.62934 88.30457 89.95048 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82665 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36578 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 26678 mr = 56008 m= 2665 mr = 18074 m= 72 mr = 1177 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1137 time to turn everything in is 0.4000000 number of dielectric boundary points 36822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 483 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 28841 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) : 0.5346228 object centre at (A) : -16.09750 7.685499 -44.07050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4147186E-02 -4.5312280E-03 midg,1,midg; midg,igrid,midg -4.7739893E-03 4.8432699E-03 1,midg,midg; igrid,midg,midg 5.1244469E-03 1.6372483E-02 gauss-seidel spectral radius is 0.9982296 estimated iterations to convergence 189 setup time was (sec) 0.6200000 now iterating at: 18:46:54 rms-change max change #iterations 3.787038 165.9088 at 10iterations 1.591365 57.80276 at 20iterations 0.6731935 25.08246 at 30iterations 0.2835017 10.37733 at 40iterations 0.1198325 4.126007 at 50iterations 5.0530080E-02 1.602882 at 60iterations 2.1277219E-02 0.7256584 at 70iterations 8.9977812E-03 0.3139038 at 80iterations 3.8064611E-03 0.1256790 at 90iterations 1.6180036E-03 5.3410292E-02 at 100iterations 6.9076638E-04 2.5213242E-02 at 110iterations 3.0043267E-04 1.0505676E-02 at 120iterations finished qdiffx linear iterations at : 18:47:01 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 3.0043267E-04 1.0505676E-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) 7.890000 DelPhi exited at 18:47:02 7.888u 0.204s 0:08.62 93.7% 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 Mon Oct 10 2011 at 18:47:02 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3919 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: 2.405803 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): -42.76000 10.56500 ymin,ymax (A): -18.38400 33.75500 zmin,zma (A): -77.36500 -10.77600 x,y,z range (A): 53.32500 52.13900 66.58900 scale (grids/A): 2.405803 object centre (A): -16.09750 7.685499 -44.07050 number of atom coordinates read : 3919 total number of charged atoms : 3777 net assigned charge : 7.000044 assigned positive charge : 601.5421 centred at (gu) : 88.05862 88.09164 89.71601 assigned negative charge : -594.5452 centred at (gu) : 87.94392 87.45678 89.92581 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 191929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36578 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 91797 mr = 137277 m= 26194 mr = 71885 m= 3829 mr = 19272 m= 226 mr = 2343 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 3987 time to turn everything in is 0.9900000 number of dielectric boundary points 83132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 46 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 30178 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) : 1.603869 object centre at (A) : -16.09750 7.685499 -44.07050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6187042 8.2583772E-03 midg,1,midg; midg,igrid,midg -6.8210833E-02 3.7451420E-02 1,midg,midg; igrid,midg,midg 0.1213823 0.3108342 gauss-seidel spectral radius is 0.9991847 estimated iterations to convergence 277 setup time was (sec) 1.220000 now iterating at: 18:47:04 rms-change max change #iterations 9.937457 363.2386 at 10iterations 5.701758 145.9936 at 20iterations 3.243274 70.84538 at 30iterations 1.842277 39.82036 at 40iterations 1.042481 21.54906 at 50iterations 0.5876078 11.30791 at 60iterations 0.3308140 7.327143 at 70iterations 0.1857610 4.199913 at 80iterations 0.1044954 2.012148 at 90iterations 5.8569245E-02 1.236206 at 100iterations 3.2848287E-02 0.6589813 at 110iterations 1.8427271E-02 0.4031346 at 120iterations 1.0377014E-02 0.2127495 at 130iterations 5.8638360E-03 0.1182632 at 140iterations 3.3395565E-03 6.7872047E-02 at 150iterations 1.9413709E-03 4.4911385E-02 at 160iterations 1.1758493E-03 2.8396606E-02 at 170iterations 7.6297374E-04 1.7093658E-02 at 180iterations finished qdiffx linear iterations at : 18:47:15 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 7.6297374E-04 1.7093658E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.85000 DelPhi exited at 18:47:16 12.856u 0.218s 0:13.36 97.7% 0+0k 0+0io 0pf+0w