Tue Oct 11 07:59:07 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 07:59:07 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 = 4030 !!! WARNING: ASN 1035 has a net charge of -0.2720 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: 0.5309708 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): -64.14800 -5.983000 ymin,ymax (A): 136.3480 203.3950 zmin,zma (A): 49.32400 108.2380 x,y,z range (A): 58.16500 67.04700 58.91400 scale (grids/A): 0.5309708 object centre (A): -35.06550 169.8715 78.78100 number of atom coordinates read : 4030 total number of charged atoms : 3883 net assigned charge : 12.72802 assigned positive charge : 618.4499 centred at (gu) : 89.28049 90.35738 89.34663 assigned negative charge : -605.7252 centred at (gu) : 89.29292 90.38477 89.31556 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7337 nv = 96 ne = 84 npr = 78582 no. pairs analyzed = 78582 no. exposed pairs = 5336 no. arc points = 37299 no. surface atoms = 1782 nbur = 2248 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 = 1.624000 m= 276 mr = 3678 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3929 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3819 ## 597 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 9792 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2265154E-10 5.0270232E-10 midg,1,midg; midg,igrid,midg 5.2411298E-10 3.2107320E-10 1,midg,midg; igrid,midg,midg 5.9487409E-10 3.1129860E-10 gauss-seidel spectral radius is 0.9818047 estimated iterations to convergence 61 setup time was (sec) 0.4700000 now iterating at: 07:59:08 rms-change max change #iterations 7.6023564E-02 12.08575 at 10iterations 4.6741888E-03 0.6755447 at 20iterations 4.4067050E-04 5.4780960E-02 at 30iterations 1.2805597E-04 1.3910294E-02 at 40iterations 4.8766386E-05 5.0978661E-03 at 50iterations finished qdiffx linear iterations at : 07:59:11 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 4.8766386E-05 5.0978661E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 07:59:13 3.547u 0.186s 0:05.87 63.3% 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 07:59:13 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 = 4030 !!! WARNING: ASN 1035 has a net charge of -0.2720 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: 1.592913 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): -64.14800 -5.983000 ymin,ymax (A): 136.3480 203.3950 zmin,zma (A): 49.32400 108.2380 x,y,z range (A): 58.16500 67.04700 58.91400 scale (grids/A): 1.592913 object centre (A): -35.06550 169.8715 78.78100 number of atom coordinates read : 4030 total number of charged atoms : 3883 net assigned charge : 12.72802 assigned positive charge : 618.4499 centred at (gu) : 87.84009 91.07098 88.03864 assigned negative charge : -605.7252 centred at (gu) : 87.87839 91.15396 87.94640 start vw surface at 0.1300000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 82057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37299 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 24359 mr = 55178 m= 2325 mr = 15884 m= 51 mr = 923 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 36808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 514 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 29483 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) : 0.5309708 object centre at (A) : -35.06550 169.8715 78.78100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1083348E-02 1.4752227E-02 midg,1,midg; midg,igrid,midg 1.0293773E-02 -4.9672714E-03 1,midg,midg; igrid,midg,midg 1.4074715E-02 9.2712399E-03 gauss-seidel spectral radius is 0.9982074 estimated iterations to convergence 188 setup time was (sec) 0.6300000 now iterating at: 07:59:14 rms-change max change #iterations 3.760870 164.4894 at 10iterations 1.573231 54.21035 at 20iterations 0.6617392 20.48104 at 30iterations 0.2784619 9.998901 at 40iterations 0.1169742 4.242400 at 50iterations 4.9389694E-02 1.640574 at 60iterations 2.0674100E-02 0.6527901 at 70iterations 8.7227784E-03 0.2900820 at 80iterations 3.6709178E-03 0.1185770 at 90iterations 1.5587572E-03 5.1744461E-02 at 100iterations 6.6242274E-04 2.0647049E-02 at 110iterations 2.8771910E-04 1.0147095E-02 at 120iterations finished qdiffx linear iterations at : 07:59:21 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.8771910E-04 1.0147095E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 07:59:22 7.963u 0.221s 0:09.13 89.5% 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 07:59:22 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 = 4030 !!! WARNING: ASN 1035 has a net charge of -0.2720 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: 2.389369 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): -64.14800 -5.983000 ymin,ymax (A): 136.3480 203.3950 zmin,zma (A): 49.32400 108.2380 x,y,z range (A): 58.16500 67.04700 58.91400 scale (grids/A): 2.389369 object centre (A): -35.06550 169.8715 78.78100 number of atom coordinates read : 4030 total number of charged atoms : 3883 net assigned charge : 12.72802 assigned positive charge : 618.4499 centred at (gu) : 86.75982 91.60622 87.05789 assigned negative charge : -605.7252 centred at (gu) : 86.81748 91.73077 86.91949 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 190256 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37299 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 86363 mr = 135100 m= 22877 mr = 66671 m= 3347 mr = 16214 m= 181 mr = 1881 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9700000 number of dielectric boundary points 83119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 30990 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) : 1.592913 object centre at (A) : -35.06550 169.8715 78.78100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1558454 0.2196292 midg,1,midg; midg,igrid,midg 5.1764462E-02 -3.4472317E-02 1,midg,midg; igrid,midg,midg 0.1990767 0.1302868 gauss-seidel spectral radius is 0.9991854 estimated iterations to convergence 277 setup time was (sec) 1.210000 now iterating at: 07:59:24 rms-change max change #iterations 10.11121 271.9647 at 10iterations 5.915549 145.1851 at 20iterations 3.412733 84.13712 at 30iterations 1.959882 41.18337 at 40iterations 1.123753 24.59199 at 50iterations 0.6405225 13.83947 at 60iterations 0.3637390 7.759591 at 70iterations 0.2061682 4.273590 at 80iterations 0.1165244 2.426643 at 90iterations 6.5975532E-02 1.305645 at 100iterations 3.7181772E-02 0.7380028 at 110iterations 2.0948108E-02 0.4391911 at 120iterations 1.1813360E-02 0.2250252 at 130iterations 6.6521415E-03 0.1391993 at 140iterations 3.7358971E-03 7.8769684E-02 at 150iterations 2.1008151E-03 4.5299530E-02 at 160iterations 1.1840087E-03 2.2777557E-02 at 170iterations 6.6660304E-04 1.2447834E-02 at 180iterations finished qdiffx linear iterations at : 07:59:35 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 6.6660304E-04 1.2447834E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 07:59:36 12.765u 0.230s 0:13.79 94.1% 0+0k 0+0io 0pf+0w