Mon Oct 10 14:01:44 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 14:01:44 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3270 !!! WARNING: SEP 64 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6014631 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): -10.98500 45.11700 ymin,ymax (A): -12.65800 39.16800 zmin,zma (A): -20.59300 38.59600 x,y,z range (A): 56.10200 51.82600 59.18900 scale (grids/A): 0.6014631 object centre (A): 17.06600 13.25500 9.001500 number of atom coordinates read : 3270 total number of charged atoms : 3124 net assigned charge : 2.025012 assigned positive charge : 492.0159 centred at (gu) : 90.90282 89.22567 90.29335 assigned negative charge : -489.9920 centred at (gu) : 91.00633 89.19087 90.28205 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7764 nv = 96 ne = 84 npr = 67742 no. pairs analyzed = 67742 no. exposed pairs = 3879 no. arc points = 26612 no. surface atoms = 1300 nbur = 1970 mkacc time = 0.1900000 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 = 1.456000 m= 359 mr = 4373 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.4300000 number of dielectric boundary points 3714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2627 ## 266 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 9708 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0502468E-10 1.6211111E-09 midg,1,midg; midg,igrid,midg -8.5619239E-10 2.2193014E-09 1,midg,midg; igrid,midg,midg 4.8027484E-09 -5.0291331E-09 gauss-seidel spectral radius is 0.9857451 estimated iterations to convergence 69 setup time was (sec) 0.8000000 now iterating at: 14:01:45 rms-change max change #iterations 0.1264531 21.40428 at 10iterations 1.1062409E-02 1.728315 at 20iterations 1.0157258E-03 0.1320972 at 30iterations 1.1670944E-04 1.7749786E-02 at 40iterations 2.1530279E-05 3.8042068E-03 at 50iterations finished qdiffx linear iterations at : 14:01:50 total time elapsed so far: 5.880000 # loops : 50 mean,max change (kT/e) : 2.1530279E-05 3.8042068E-03 energy calculations done at 5.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.080000 DelPhi exited at 14:01:51 6.081u 0.522s 0:07.18 91.9% 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 Mon Oct 10 2011 at 14:01:51 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3270 !!! WARNING: SEP 64 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.804389 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): -10.98500 45.11700 ymin,ymax (A): -12.65800 39.16800 zmin,zma (A): -20.59300 38.59600 x,y,z range (A): 56.10200 51.82600 59.18900 scale (grids/A): 1.804389 object centre (A): 17.06600 13.25500 9.001500 number of atom coordinates read : 3270 total number of charged atoms : 3124 net assigned charge : 2.025012 assigned positive charge : 492.0159 centred at (gu) : 92.70767 87.67643 90.87925 assigned negative charge : -489.9920 centred at (gu) : 93.01875 87.57224 90.84565 start vw surface at 0.1800000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 85831 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26612 grid for indexing accessible points = 1.400000 m= 28884 mr = 60922 m= 3715 mr = 20970 m= 162 mr = 2199 m= 4 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1584 time to turn everything in is 0.7800000 number of dielectric boundary points 34447 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 24419 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) : 0.6014631 object centre at (A) : 17.06600 13.25500 9.001500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2013467E-03 3.0236742E-02 midg,1,midg; midg,igrid,midg 4.8254938E-03 3.2041353E-05 1,midg,midg; igrid,midg,midg 2.0811129E-02 -9.5719248E-03 gauss-seidel spectral radius is 0.9985461 estimated iterations to convergence 208 setup time was (sec) 1.190000 now iterating at: 14:01:53 rms-change max change #iterations 4.347683 208.6762 at 10iterations 1.976739 62.29965 at 20iterations 0.9024034 27.11626 at 30iterations 0.4127665 11.84485 at 40iterations 0.1888201 5.972542 at 50iterations 8.6180799E-02 2.484932 at 60iterations 3.9505504E-02 1.201068 at 70iterations 1.8078808E-02 0.5743980 at 80iterations 8.2853585E-03 0.2332211 at 90iterations 3.8000236E-03 0.1187954 at 100iterations 1.7451363E-03 5.0827026E-02 at 110iterations 8.0294872E-04 2.5617123E-02 at 120iterations finished qdiffx linear iterations at : 14:02:06 total time elapsed so far: 14.40000 # loops : 120 mean,max change (kT/e) : 8.0294872E-04 2.5617123E-02 energy calculations done at 14.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.58000 DelPhi exited at 14:02:08 14.581u 0.605s 0:16.53 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 Mon Oct 10 2011 at 14:02:08 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3270 !!! WARNING: SEP 64 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.706584 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): -10.98500 45.11700 ymin,ymax (A): -12.65800 39.16800 zmin,zma (A): -20.59300 38.59600 x,y,z range (A): 56.10200 51.82600 59.18900 scale (grids/A): 2.706584 object centre (A): 17.06600 13.25500 9.001500 number of atom coordinates read : 3270 total number of charged atoms : 3124 net assigned charge : 2.025012 assigned positive charge : 492.0159 centred at (gu) : 94.06132 86.51440 91.31873 assigned negative charge : -489.9920 centred at (gu) : 94.52802 86.35821 91.26837 start vw surface at 0.1700000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 198962 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26612 grid for indexing accessible points = 1.400000 m= 97507 mr = 147813 m= 31213 mr = 79653 m= 6184 mr = 24362 m= 780 mr = 4587 m= 36 mr = 501 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 5308 time to turn everything in is 1.900000 number of dielectric boundary points 77762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 24989 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) : 1.804389 object centre at (A) : 17.06600 13.25500 9.001500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2037636 0.3795949 midg,1,midg; midg,igrid,midg 0.1224487 -2.1433201E-02 1,midg,midg; igrid,midg,midg 0.3832066 -7.6081073E-03 gauss-seidel spectral radius is 0.9992490 estimated iterations to convergence 288 setup time was (sec) 2.220000 now iterating at: 14:02:10 rms-change max change #iterations 10.49572 285.0800 at 10iterations 6.154363 133.4863 at 20iterations 3.569871 74.49983 at 30iterations 2.075695 50.86945 at 40iterations 1.197738 22.40743 at 50iterations 0.6924006 12.38068 at 60iterations 0.3988696 7.484716 at 70iterations 0.2288246 3.905888 at 80iterations 0.1316790 2.500493 at 90iterations 7.5734720E-02 1.366837 at 100iterations 4.3447051E-02 0.7487013 at 110iterations 2.4941489E-02 0.4167175 at 120iterations 1.4324943E-02 0.2555408 at 130iterations 8.2190000E-03 0.1463175 at 140iterations 4.7231698E-03 9.6311569E-02 at 150iterations 2.7135562E-03 5.0631523E-02 at 160iterations 1.5675292E-03 2.7198792E-02 at 170iterations 9.0577616E-04 1.5768051E-02 at 180iterations finished qdiffx linear iterations at : 14:02:24 total time elapsed so far: 16.18000 # loops : 180 mean,max change (kT/e) : 9.0577616E-04 1.5768051E-02 energy calculations done at 16.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.36000 DelPhi exited at 14:02:25 16.360u 0.432s 0:17.13 98.0% 0+0k 0+0io 0pf+0w