Sun Oct 9 15:00:42 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 Sun Oct 9 2011 at 15:00:42 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1137 !!! WARNING: HIR 87 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.8583484 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): -63.19700 -21.72200 ymin,ymax (A): 23.16300 57.47400 zmin,zma (A): 11.14200 48.64600 x,y,z range (A): 41.47500 34.31100 37.50400 scale (grids/A): 0.8583484 object centre (A): -42.45950 40.31850 29.89400 number of atom coordinates read : 1137 total number of charged atoms : 1009 net assigned charge : 2.514005 assigned positive charge : 165.6092 centred at (gu) : 89.46951 91.70605 90.71854 assigned negative charge : -163.0951 centred at (gu) : 89.49977 91.80245 90.37716 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5924 nv = 96 ne = 84 npr = 23648 no. pairs analyzed = 23648 no. exposed pairs = 1488 no. arc points = 10572 no. surface atoms = 505 nbur = 632 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 534 mr = 3258 m= 5 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.2100000 number of dielectric boundary points 3070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 587 ## 51 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5120 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2695626E-07 2.0056900E-06 midg,1,midg; midg,igrid,midg 6.0912487E-07 -7.3140813E-09 1,midg,midg; igrid,midg,midg 5.7763100E-07 2.5837795E-07 gauss-seidel spectral radius is 0.9928104 estimated iterations to convergence 95 setup time was (sec) 0.4800000 now iterating at: 15:00:43 rms-change max change #iterations 0.3060155 38.79916 at 10iterations 5.3804878E-02 8.175800 at 20iterations 9.3551455E-03 1.208920 at 30iterations 1.6171106E-03 0.2140198 at 40iterations 2.8683504E-04 4.1605473E-02 at 50iterations finished qdiffx linear iterations at : 15:00:46 total time elapsed so far: 3.730000 # loops : 50 mean,max change (kT/e) : 2.8683504E-04 4.1605473E-02 energy calculations done at 3.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.910000 DelPhi exited at 15:00:47 3.912u 0.260s 0:04.43 94.1% 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 15:00:47 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1137 !!! WARNING: HIR 87 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.575045 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): -63.19700 -21.72200 ymin,ymax (A): 23.16300 57.47400 zmin,zma (A): 11.14200 48.64600 x,y,z range (A): 41.47500 34.31100 37.50400 scale (grids/A): 2.575045 object centre (A): -42.45950 40.31850 29.89400 number of atom coordinates read : 1137 total number of charged atoms : 1009 net assigned charge : 2.514005 assigned positive charge : 165.6092 centred at (gu) : 88.40884 95.11835 92.15578 assigned negative charge : -163.0951 centred at (gu) : 88.49944 95.40754 91.13165 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 60795 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10572 grid for indexing accessible points = 1.400000 m= 26385 mr = 41173 m= 7035 mr = 20397 m= 1059 mr = 5103 m= 93 mr = 653 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1634 time to turn everything in is 0.6100000 number of dielectric boundary points 27988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 8067 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) : 0.8583484 object centre at (A) : -42.45950 40.31850 29.89400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6726169E-02 8.6031854E-02 midg,1,midg; midg,igrid,midg 2.2350917E-02 -1.3115747E-02 1,midg,midg; igrid,midg,midg 2.3643589E-03 2.1298291E-02 gauss-seidel spectral radius is 0.9990665 estimated iterations to convergence 259 setup time was (sec) 0.9000000 now iterating at: 15:00:48 rms-change max change #iterations 4.571645 242.1987 at 10iterations 2.442407 94.99993 at 20iterations 1.300300 42.79177 at 30iterations 0.6944358 24.24191 at 40iterations 0.3699462 11.83572 at 50iterations 0.1972423 6.276030 at 60iterations 0.1051884 3.121056 at 70iterations 5.6204710E-02 1.636611 at 80iterations 2.9921738E-02 0.9622672 at 90iterations 1.5996316E-02 0.5104885 at 100iterations 8.5125091E-03 0.2732925 at 110iterations 4.5300014E-03 0.1547031 at 120iterations finished qdiffx linear iterations at : 15:00:56 total time elapsed so far: 9.100000 # loops : 120 mean,max change (kT/e) : 4.5300014E-03 0.1547031 energy calculations done at 9.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.270000 DelPhi exited at 15:00:57 9.272u 0.288s 0:09.81 97.3% 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 Sun Oct 9 2011 at 15:00:57 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1137 !!! WARNING: HIR 87 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.862568 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): -63.19700 -21.72200 ymin,ymax (A): 23.16300 57.47400 zmin,zma (A): 11.14200 48.64600 x,y,z range (A): 41.47500 34.31100 37.50400 scale (grids/A): 3.862568 object centre (A): -42.45950 40.31850 29.89400 number of atom coordinates read : 1137 total number of charged atoms : 1009 net assigned charge : 2.514005 assigned positive charge : 165.6092 centred at (gu) : 87.61325 97.67754 93.23377 assigned negative charge : -163.0951 centred at (gu) : 87.74908 98.11132 91.69751 start vw surface at 0.1000000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 139243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10572 grid for indexing accessible points = 1.400000 m= 77106 mr = 98411 m= 37633 mr = 64531 m= 14093 mr = 31685 m= 3979 mr = 11465 m= 856 mr = 3163 m= 133 mr = 630 m= 6 mr = 107 m= 0 mr = 3 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 5546 time to turn everything in is 1.940000 number of dielectric boundary points 63054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 8072 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) : 2.575045 object centre at (A) : -42.45950 40.31850 29.89400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4302001 0.4278679 midg,1,midg; midg,igrid,midg 5.4888401E-02 -0.2084671 1,midg,midg; igrid,midg,midg -0.1138986 0.1900520 gauss-seidel spectral radius is 0.9993368 estimated iterations to convergence 306 setup time was (sec) 2.250000 now iterating at: 15:00:59 rms-change max change #iterations 9.389148 231.5055 at 10iterations 5.579624 115.5221 at 20iterations 3.311570 64.37595 at 30iterations 1.966087 37.80010 at 40iterations 1.168540 21.40287 at 50iterations 0.6921983 11.90061 at 60iterations 0.4101435 7.397945 at 70iterations 0.2430511 4.590515 at 80iterations 0.1436857 2.421327 at 90iterations 8.5324049E-02 1.706030 at 100iterations 5.0552409E-02 1.045872 at 110iterations 2.9832428E-02 0.5221519 at 120iterations 1.7654570E-02 0.3216095 at 130iterations 1.0462884E-02 0.1970234 at 140iterations 6.1889552E-03 9.7152710E-02 at 150iterations 3.6597399E-03 6.7384720E-02 at 160iterations 2.1645385E-03 3.7818909E-02 at 170iterations 1.2804769E-03 2.3698807E-02 at 180iterations finished qdiffx linear iterations at : 15:01:13 total time elapsed so far: 15.52000 # loops : 180 mean,max change (kT/e) : 1.2804769E-03 2.3698807E-02 energy calculations done at 15.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.69000 DelPhi exited at 15:01:13 15.689u 0.330s 0:16.28 98.3% 0+0k 0+0io 0pf+0w