Sun Oct 9 10:33:53 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 10:33:53 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2959 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: CME 217 has a net charge of -0.3480 !!! WARNING: CME 312 has a net charge of -0.3480 !!! WARNING: CME 456 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 0.5822512 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): -22.05900 39.08300 ymin,ymax (A): -25.34600 24.20900 zmin,zma (A): -28.78300 26.57400 x,y,z range (A): 61.14200 49.55500 55.35700 scale (grids/A): 0.5822512 object centre (A): 8.512000 -0.5684996 -1.104500 number of atom coordinates read : 2959 total number of charged atoms : 2834 net assigned charge : 0.4330308 assigned positive charge : 434.1069 centred at (gu) : 89.75072 91.16061 91.32770 assigned negative charge : -433.6757 centred at (gu) : 89.68459 91.08296 91.28422 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6849 nv = 96 ne = 84 npr = 58534 no. pairs analyzed = 58534 no. exposed pairs = 4002 no. arc points = 27816 no. surface atoms = 1324 nbur = 1635 mkacc time = 0.1200000 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 = 1.484000 m= 360 mr = 3488 m= 3 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2789 ## 282 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8667 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8556411E-10 1.4642351E-09 midg,1,midg; midg,igrid,midg -1.3211258E-09 2.4322764E-09 1,midg,midg; igrid,midg,midg -1.5586679E-09 1.4921374E-09 gauss-seidel spectral radius is 0.9847848 estimated iterations to convergence 67 setup time was (sec) 0.5300000 now iterating at: 10:33:54 rms-change max change #iterations 9.7858652E-02 17.63046 at 10iterations 8.0482690E-03 1.185347 at 20iterations 9.2376879E-04 0.1501999 at 30iterations 2.1406895E-04 3.6119461E-02 at 40iterations 6.4331252E-05 1.0941505E-02 at 50iterations finished qdiffx linear iterations at : 10:33:56 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 6.4331252E-05 1.0941505E-02 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 10:33:57 3.157u 0.161s 0:03.69 89.7% 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 Sun Oct 9 2011 at 10:33:57 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2959 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: CME 217 has a net charge of -0.3480 !!! WARNING: CME 312 has a net charge of -0.3480 !!! WARNING: CME 456 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 1.746753 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): -22.05900 39.08300 ymin,ymax (A): -25.34600 24.20900 zmin,zma (A): -28.78300 26.57400 x,y,z range (A): 61.14200 49.55500 55.35700 scale (grids/A): 1.746753 object centre (A): 8.512000 -0.5684996 -1.104500 number of atom coordinates read : 2959 total number of charged atoms : 2834 net assigned charge : 0.4330308 assigned positive charge : 434.1069 centred at (gu) : 89.25138 93.48065 93.98193 assigned negative charge : -433.6757 centred at (gu) : 89.05362 93.24852 93.85242 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 75617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27816 grid for indexing accessible points = 1.400000 m= 24916 mr = 51367 m= 3389 mr = 16837 m= 158 mr = 1690 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 245 time to turn everything in is 0.5100000 number of dielectric boundary points 34157 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 22065 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) : 0.5822512 object centre at (A) : 8.512000 -0.5684996 -1.104500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5353950E-03 7.8293402E-03 midg,1,midg; midg,igrid,midg -5.8659835E-04 2.0882573E-02 1,midg,midg; igrid,midg,midg -1.2866278E-03 -3.9745434E-03 gauss-seidel spectral radius is 0.9984381 estimated iterations to convergence 201 setup time was (sec) 0.7700000 now iterating at: 10:33:58 rms-change max change #iterations 3.787000 177.8776 at 10iterations 1.673984 60.44510 at 20iterations 0.7442968 25.41971 at 30iterations 0.3304970 10.52507 at 40iterations 0.1470873 4.933548 at 50iterations 6.5141641E-02 2.216591 at 60iterations 2.8992722E-02 0.9173355 at 70iterations 1.2989286E-02 0.4612389 at 80iterations 5.8329264E-03 0.1963654 at 90iterations 2.6555515E-03 8.8928223E-02 at 100iterations 1.2410553E-03 4.3251038E-02 at 110iterations 6.0482847E-04 2.0856857E-02 at 120iterations finished qdiffx linear iterations at : 10:34:04 total time elapsed so far: 6.840000 # loops : 120 mean,max change (kT/e) : 6.0482847E-04 2.0856857E-02 energy calculations done at 6.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 10:34:04 7.011u 0.209s 0:07.53 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 Sun Oct 9 2011 at 10:34:04 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2959 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: CME 217 has a net charge of -0.3480 !!! WARNING: CME 312 has a net charge of -0.3480 !!! WARNING: CME 456 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 2.620130 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): -22.05900 39.08300 ymin,ymax (A): -25.34600 24.20900 zmin,zma (A): -28.78300 26.57400 x,y,z range (A): 61.14200 49.55500 55.35700 scale (grids/A): 2.620130 object centre (A): 8.512000 -0.5684996 -1.104500 number of atom coordinates read : 2959 total number of charged atoms : 2834 net assigned charge : 0.4330308 assigned positive charge : 434.1069 centred at (gu) : 88.87695 95.22074 95.97292 assigned negative charge : -433.6757 centred at (gu) : 88.58036 94.87281 95.77870 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 175479 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27816 grid for indexing accessible points = 1.400000 m= 83019 mr = 125946 m= 26775 mr = 64864 m= 5515 mr = 19795 m= 589 mr = 3449 m= 18 mr = 306 m= 0 mr = 2 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 733 time to turn everything in is 1.270000 number of dielectric boundary points 77033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 22665 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) : 1.746753 object centre at (A) : 8.512000 -0.5684996 -1.104500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0473676E-02 0.1056209 midg,1,midg; midg,igrid,midg 5.6616131E-02 0.2888358 1,midg,midg; igrid,midg,midg 8.6355999E-02 -9.0045474E-02 gauss-seidel spectral radius is 0.9992170 estimated iterations to convergence 282 setup time was (sec) 1.560000 now iterating at: 10:34:06 rms-change max change #iterations 9.428818 257.8043 at 10iterations 5.490333 142.9151 at 20iterations 3.171053 72.98258 at 30iterations 1.821010 41.94611 at 40iterations 1.043889 25.61928 at 50iterations 0.5954298 13.20110 at 60iterations 0.3395986 7.023596 at 70iterations 0.1932120 3.751783 at 80iterations 0.1098230 2.358589 at 90iterations 6.2389296E-02 1.214847 at 100iterations 3.5355151E-02 0.7167654 at 110iterations 2.0090858E-02 0.3963089 at 120iterations 1.1407344E-02 0.2103653 at 130iterations 6.4814091E-03 0.1238518 at 140iterations 3.6919562E-03 7.0091248E-02 at 150iterations 2.1179193E-03 3.9939880E-02 at 160iterations 1.2240498E-03 2.6872635E-02 at 170iterations 7.2114810E-04 1.4552116E-02 at 180iterations finished qdiffx linear iterations at : 10:34:16 total time elapsed so far: 11.14000 # loops : 180 mean,max change (kT/e) : 7.2114810E-04 1.4552116E-02 energy calculations done at 11.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.31000 DelPhi exited at 10:34:16 11.313u 0.216s 0:12.14 94.8% 0+0k 0+0io 0pf+0w