Tue Oct 11 03:20:58 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 03:20:58 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: 369 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3462 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SEP 224 has a net charge of -0.4750 !!! WARNING: SER 496 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5790783 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): -10.18400 43.06900 ymin,ymax (A): 14.67700 75.58200 zmin,zma (A): 40.12700 101.6040 x,y,z range (A): 53.25300 60.90500 61.47700 scale (grids/A): 0.5790783 object centre (A): 16.44250 45.12950 70.86550 number of atom coordinates read : 3462 total number of charged atoms : 3315 net assigned charge : -7.087972 assigned positive charge : 525.3914 centred at (gu) : 88.28667 87.63801 88.39240 assigned negative charge : -532.4808 centred at (gu) : 88.30232 87.62750 88.37456 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7612 nv = 96 ne = 84 npr = 70921 no. pairs analyzed = 70921 no. exposed pairs = 4304 no. arc points = 29968 no. surface atoms = 1438 nbur = 2024 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= 392 mr = 4118 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.2500000 number of dielectric boundary points 3851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3058 ## 336 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9690 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7924660E-09 -7.1887285E-10 midg,1,midg; midg,igrid,midg -3.0056668E-09 -7.1621437E-10 1,midg,midg; igrid,midg,midg -1.5850787E-09 -1.2660251E-09 gauss-seidel spectral radius is 0.9846453 estimated iterations to convergence 66 setup time was (sec) 0.4300000 now iterating at: 03:20:59 rms-change max change #iterations 0.1120354 15.40768 at 10iterations 9.0617929E-03 1.438688 at 20iterations 8.4786944E-04 0.1117678 at 30iterations 1.3574431E-04 1.3903141E-02 at 40iterations 3.1129315E-05 2.9067993E-03 at 50iterations finished qdiffx linear iterations at : 03:21:02 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 3.1129315E-05 2.9067993E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 03:21:02 3.440u 0.199s 0:04.00 90.7% 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 Tue Oct 11 2011 at 03:21:02 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: 369 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3462 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SEP 224 has a net charge of -0.4750 !!! WARNING: SER 496 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.737235 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): -10.18400 43.06900 ymin,ymax (A): 14.67700 75.58200 zmin,zma (A): 40.12700 101.6040 x,y,z range (A): 53.25300 60.90500 61.47700 scale (grids/A): 1.737235 object centre (A): 16.44250 45.12950 70.86550 number of atom coordinates read : 3462 total number of charged atoms : 3315 net assigned charge : -7.087972 assigned positive charge : 525.3914 centred at (gu) : 84.85914 82.91357 85.17651 assigned negative charge : -532.4808 centred at (gu) : 84.90651 82.88197 85.12315 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29968 grid for indexing accessible points = 1.400000 m= 29367 mr = 56587 m= 3824 mr = 21449 m= 152 mr = 2125 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1218 time to turn everything in is 0.4000000 number of dielectric boundary points 35618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 287 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 25674 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) : 0.5790783 object centre at (A) : 16.44250 45.12950 70.86550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1725178E-02 3.9422974E-02 midg,1,midg; midg,igrid,midg -1.3173167E-02 4.0811468E-03 1,midg,midg; igrid,midg,midg -6.9724992E-03 -8.2466425E-04 gauss-seidel spectral radius is 0.9984401 estimated iterations to convergence 201 setup time was (sec) 0.6200000 now iterating at: 03:21:03 rms-change max change #iterations 4.228388 155.8532 at 10iterations 1.865305 75.81217 at 20iterations 0.8293453 30.95473 at 30iterations 0.3680842 12.61895 at 40iterations 0.1637146 5.272331 at 50iterations 7.2676666E-02 2.232164 at 60iterations 3.2340720E-02 1.044830 at 70iterations 1.4375993E-02 0.4774618 at 80iterations 6.4252857E-03 0.2064857 at 90iterations 2.8693385E-03 9.5300674E-02 at 100iterations 1.2836976E-03 3.9697647E-02 at 110iterations 5.7984318E-04 1.8255115E-02 at 120iterations finished qdiffx linear iterations at : 03:21:10 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 5.7984318E-04 1.8255115E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 03:21:11 7.852u 0.215s 0:08.58 93.9% 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 03:21:11 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: 369 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3462 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SEP 224 has a net charge of -0.4750 !!! WARNING: SER 496 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.605853 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): -10.18400 43.06900 ymin,ymax (A): 14.67700 75.58200 zmin,zma (A): 40.12700 101.6040 x,y,z range (A): 53.25300 60.90500 61.47700 scale (grids/A): 2.605853 object centre (A): 16.44250 45.12950 70.86550 number of atom coordinates read : 3462 total number of charged atoms : 3315 net assigned charge : -7.087972 assigned positive charge : 525.3914 centred at (gu) : 82.28861 79.37007 82.76447 assigned negative charge : -532.4808 centred at (gu) : 82.35967 79.32268 82.68458 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 190742 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29968 grid for indexing accessible points = 1.400000 m= 95361 mr = 137401 m= 32946 mr = 77353 m= 6513 mr = 26217 m= 640 mr = 4610 m= 30 mr = 344 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 4344 time to turn everything in is 1.010000 number of dielectric boundary points 80307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 26506 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) : 1.737235 object centre at (A) : 16.44250 45.12950 70.86550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4026545 0.8714947 midg,1,midg; midg,igrid,midg -0.3073936 0.2569402 1,midg,midg; igrid,midg,midg -5.7741418E-02 -1.8835455E-02 gauss-seidel spectral radius is 0.9992261 estimated iterations to convergence 284 setup time was (sec) 1.250000 now iterating at: 03:21:12 rms-change max change #iterations 10.39656 323.0949 at 10iterations 6.033671 174.8769 at 20iterations 3.469492 78.14388 at 30iterations 1.993113 47.70399 at 40iterations 1.138774 25.90876 at 50iterations 0.6498933 13.63702 at 60iterations 0.3699075 7.286080 at 70iterations 0.2117327 4.574766 at 80iterations 0.1204406 2.275711 at 90iterations 6.8596408E-02 1.476524 at 100iterations 3.9004181E-02 0.7340256 at 110iterations 2.2179445E-02 0.4084425 at 120iterations 1.2608065E-02 0.2246134 at 130iterations 7.1661673E-03 0.1269894 at 140iterations 4.0872954E-03 8.1978321E-02 at 150iterations 2.3334706E-03 4.9810410E-02 at 160iterations 1.3281058E-03 2.2804260E-02 at 170iterations 7.6296402E-04 1.3748169E-02 at 180iterations finished qdiffx linear iterations at : 03:21:24 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 7.6296402E-04 1.3748169E-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 03:21:24 12.854u 0.257s 0:13.51 96.9% 0+0k 0+0io 0pf+0w