Tue Oct 11 08:32:25 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 Tue Oct 11 2011 at 08:32:25 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2747 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6727644 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): -17.83900 35.07700 ymin,ymax (A): -1.023000 50.64800 zmin,zma (A): -16.86000 31.21500 x,y,z range (A): 52.91600 51.67100 48.07500 scale (grids/A): 0.6727644 object centre (A): 8.618999 24.81250 7.177500 number of atom coordinates read : 2747 total number of charged atoms : 2616 net assigned charge : 3.500018 assigned positive charge : 422.7039 centred at (gu) : 89.18038 90.80531 89.58377 assigned negative charge : -419.2043 centred at (gu) : 89.07879 90.59339 89.45065 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8385 nv = 96 ne = 84 npr = 55432 no. pairs analyzed = 55432 no. exposed pairs = 3500 no. arc points = 24037 no. surface atoms = 1174 nbur = 1573 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 485 mr = 4686 m= 5 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2284 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9817 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9783910E-08 4.6928598E-08 midg,1,midg; midg,igrid,midg -4.3257433E-08 8.6856225E-08 1,midg,midg; igrid,midg,midg -2.1204192E-08 3.5581348E-08 gauss-seidel spectral radius is 0.9885598 estimated iterations to convergence 76 setup time was (sec) 0.3900000 now iterating at: 08:32:26 rms-change max change #iterations 0.1896014 31.08772 at 10iterations 2.1320514E-02 4.389477 at 20iterations 2.4469171E-03 0.3294373 at 30iterations 3.0671179E-04 3.6457062E-02 at 40iterations 4.8933238E-05 6.9465637E-03 at 50iterations finished qdiffx linear iterations at : 08:32:29 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 4.8933238E-05 6.9465637E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 08:32:29 3.339u 0.167s 0:03.80 91.8% 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 08:32:29 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2747 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.018293 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): -17.83900 35.07700 ymin,ymax (A): -1.023000 50.64800 zmin,zma (A): -16.86000 31.21500 x,y,z range (A): 52.91600 51.67100 48.07500 scale (grids/A): 2.018293 object centre (A): 8.618999 24.81250 7.177500 number of atom coordinates read : 2747 total number of charged atoms : 2616 net assigned charge : 3.500018 assigned positive charge : 422.7039 centred at (gu) : 87.54063 92.41530 88.75085 assigned negative charge : -419.2043 centred at (gu) : 87.23615 91.78004 88.35165 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 89474 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24037 grid for indexing accessible points = 1.400000 m= 33454 mr = 62385 m= 5829 mr = 24769 m= 408 mr = 3743 m= 8 mr = 157 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 814 time to turn everything in is 0.4200000 number of dielectric boundary points 38119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 20729 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) : 0.6727644 object centre at (A) : 8.618999 24.81250 7.177500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8479097E-03 4.1283026E-02 midg,1,midg; midg,igrid,midg -4.2237807E-02 7.2107941E-02 1,midg,midg; igrid,midg,midg -1.6830515E-02 1.3827558E-02 gauss-seidel spectral radius is 0.9987954 estimated iterations to convergence 228 setup time was (sec) 0.6300000 now iterating at: 08:32:30 rms-change max change #iterations 4.966755 212.6377 at 10iterations 2.426802 68.67451 at 20iterations 1.189990 34.36024 at 30iterations 0.5842941 18.38345 at 40iterations 0.2879110 7.945160 at 50iterations 0.1410347 4.748634 at 60iterations 6.9262996E-02 2.064807 at 70iterations 3.3954099E-02 0.9258442 at 80iterations 1.6641520E-02 0.4768000 at 90iterations 8.2016177E-03 0.2398515 at 100iterations 4.0444406E-03 0.1162262 at 110iterations 1.9888014E-03 5.5084229E-02 at 120iterations finished qdiffx linear iterations at : 08:32:37 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 1.9888014E-03 5.5084229E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 08:32:38 7.763u 0.200s 0:08.26 96.3% 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 08:32:38 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2747 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.027440 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): -17.83900 35.07700 ymin,ymax (A): -1.023000 50.64800 zmin,zma (A): -16.86000 31.21500 x,y,z range (A): 52.91600 51.67100 48.07500 scale (grids/A): 3.027440 object centre (A): 8.618999 24.81250 7.177500 number of atom coordinates read : 2747 total number of charged atoms : 2616 net assigned charge : 3.500018 assigned positive charge : 422.7039 centred at (gu) : 86.31078 93.62293 88.12624 assigned negative charge : -419.2043 centred at (gu) : 85.85415 92.67010 87.52739 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 206087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24037 grid for indexing accessible points = 1.400000 m= 107012 mr = 150597 m= 40577 mr = 87683 m= 10805 mr = 32901 m= 1661 mr = 8181 m= 107 mr = 1101 m= 4 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 2526 time to turn everything in is 1.150000 number of dielectric boundary points 85739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 20928 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) : 2.018293 object centre at (A) : 8.618999 24.81250 7.177500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9188845E-02 0.2049158 midg,1,midg; midg,igrid,midg -0.3835803 0.9323934 1,midg,midg; igrid,midg,midg -0.1605906 5.8924709E-02 gauss-seidel spectral radius is 0.9993045 estimated iterations to convergence 299 setup time was (sec) 1.380000 now iterating at: 08:32:39 rms-change max change #iterations 11.37215 411.2041 at 10iterations 6.757225 129.0125 at 20iterations 3.993414 84.45345 at 30iterations 2.360267 44.87193 at 40iterations 1.393767 22.09065 at 50iterations 0.8208296 14.93065 at 60iterations 0.4836259 8.687260 at 70iterations 0.2842514 4.647327 at 80iterations 0.1668573 2.657948 at 90iterations 9.7762808E-02 1.547685 at 100iterations 5.7467587E-02 0.9365802 at 110iterations 3.3734322E-02 0.5679690 at 120iterations 1.9841654E-02 0.3198128 at 130iterations 1.1631825E-02 0.1989479 at 140iterations 6.8604802E-03 0.1173019 at 150iterations 4.0640421E-03 6.6336870E-02 at 160iterations 2.4243884E-03 4.4303894E-02 at 170iterations 1.4626897E-03 2.6794434E-02 at 180iterations finished qdiffx linear iterations at : 08:32:50 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 1.4626897E-03 2.6794434E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 08:32:51 12.808u 0.202s 0:13.61 95.5% 0+0k 0+0io 0pf+0w