Wed Dec 28 11:03:37 PST 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 Wed Dec 28 2011 at 11:03:37 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1933 !!! WARNING: ASH 25 has a net charge of -0.3190 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: 0.6058234 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): -23.68500 35.07800 ymin,ymax (A): -18.72700 20.38400 zmin,zma (A): -4.027000 39.14200 x,y,z range (A): 58.76300 39.11100 43.16900 scale (grids/A): 0.6058234 object centre (A): 5.696502 0.8284998 17.55750 number of atom coordinates read : 1933 total number of charged atoms : 1800 net assigned charge : 2.681007 assigned positive charge : 286.9860 centred at (gu) : 89.62607 90.14725 90.45308 assigned negative charge : -284.3053 centred at (gu) : 89.62186 90.28352 90.64017 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 4878 nv = 96 ne = 84 npr = 39016 no. pairs analyzed = 39016 no. exposed pairs = 2534 no. arc points = 17601 no. surface atoms = 858 nbur = 1075 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 245 mr = 2626 m= 0 mr = 18 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1821 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 5907 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5773627E-09 -5.1988929E-09 midg,1,midg; midg,igrid,midg 5.5347047E-09 -3.0959570E-09 1,midg,midg; igrid,midg,midg 1.4093794E-09 1.4451911E-09 gauss-seidel spectral radius is 0.9858420 estimated iterations to convergence 69 setup time was (sec) 0.5900000 now iterating at: 11:03:37 rms-change max change #iterations 0.1008717 18.06969 at 10iterations 8.6223688E-03 1.324341 at 20iterations 7.2774995E-04 0.1188316 at 30iterations 6.3511245E-05 1.0951996E-02 at 40iterations 5.4931297E-06 8.7738037E-04 at 50iterations finished qdiffx linear iterations at : 11:03:41 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 5.4931297E-06 8.7738037E-04 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 11:03:42 4.326u 0.216s 0:05.10 88.8% 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 Wed Dec 28 2011 at 11:03:42 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1933 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.817470 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): -23.68500 35.07800 ymin,ymax (A): -18.72700 20.38400 zmin,zma (A): -4.027000 39.14200 x,y,z range (A): 58.76300 39.11100 43.16900 scale (grids/A): 1.817470 object centre (A): 5.696502 0.8284998 17.55750 number of atom coordinates read : 1933 total number of charged atoms : 1800 net assigned charge : 2.681007 assigned positive charge : 286.9860 centred at (gu) : 88.87817 90.44158 91.35932 assigned negative charge : -284.3053 centred at (gu) : 88.86578 90.85064 91.92045 start vw surface at 0.2000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 52631 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17601 grid for indexing accessible points = 1.400000 m= 19169 mr = 35853 m= 2707 mr = 14194 m= 89 mr = 1625 m= 0 mr = 21 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 22903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 14092 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) : 0.6058234 object centre at (A) : 5.696502 0.8284998 17.55750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5450310E-03 -8.6064395E-03 midg,1,midg; midg,igrid,midg 6.9497339E-03 -4.3183067E-03 1,midg,midg; igrid,midg,midg 3.5329379E-02 3.6381271E-02 gauss-seidel spectral radius is 0.9984273 estimated iterations to convergence 200 setup time was (sec) 0.9100000 now iterating at: 11:03:43 rms-change max change #iterations 3.260776 146.9649 at 10iterations 1.438657 58.54772 at 20iterations 0.6374438 23.98764 at 30iterations 0.2810223 10.34719 at 40iterations 0.1247595 4.980533 at 50iterations 5.5061948E-02 2.059692 at 60iterations 2.4380855E-02 0.9683447 at 70iterations 1.0784693E-02 0.4702339 at 80iterations 4.7864774E-03 0.1852589 at 90iterations 2.1140822E-03 8.4678650E-02 at 100iterations 9.3924074E-04 3.5636902E-02 at 110iterations 4.1576152E-04 1.6386509E-02 at 120iterations finished qdiffx linear iterations at : 11:03:52 total time elapsed so far: 9.480000 # loops : 120 mean,max change (kT/e) : 4.1576152E-04 1.6386509E-02 energy calculations done at 9.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.700000 DelPhi exited at 11:03:52 9.706u 0.372s 0:10.52 95.7% 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 Wed Dec 28 2011 at 11:03:52 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1933 !!! WARNING: ASH 25 has a net charge of -0.3190 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: 2.726205 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): -23.68500 35.07800 ymin,ymax (A): -18.72700 20.38400 zmin,zma (A): -4.027000 39.14200 x,y,z range (A): 58.76300 39.11100 43.16900 scale (grids/A): 2.726205 object centre (A): 5.696502 0.8284998 17.55750 number of atom coordinates read : 1933 total number of charged atoms : 1800 net assigned charge : 2.681007 assigned positive charge : 286.9860 centred at (gu) : 88.31720 90.66235 92.03901 assigned negative charge : -284.3053 centred at (gu) : 88.29864 91.27602 92.88084 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 121210 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17601 grid for indexing accessible points = 1.400000 m= 62245 mr = 86627 m= 22031 mr = 50886 m= 4575 mr = 17688 m= 448 mr = 3376 m= 14 mr = 276 m= 0 mr = 3 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 51667 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 14393 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) : 1.817470 object centre at (A) : 5.696502 0.8284998 17.55750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9316489E-02 -6.1858151E-02 midg,1,midg; midg,igrid,midg 5.9047684E-02 -3.8311068E-02 1,midg,midg; igrid,midg,midg 0.4107224 0.5274809 gauss-seidel spectral radius is 0.9991860 estimated iterations to convergence 277 setup time was (sec) 1.630000 now iterating at: 11:03:54 rms-change max change #iterations 7.914283 291.0068 at 10iterations 4.499473 113.1696 at 20iterations 2.541430 61.16605 at 30iterations 1.428729 33.05199 at 40iterations 0.8041559 18.64632 at 50iterations 0.4531240 9.494396 at 60iterations 0.2530911 5.750433 at 70iterations 0.1419657 3.210725 at 80iterations 7.9488367E-02 1.736622 at 90iterations 4.4435296E-02 1.005880 at 100iterations 2.4845975E-02 0.5339851 at 110iterations 1.3874551E-02 0.2962456 at 120iterations 7.7783475E-03 0.1675191 at 130iterations 4.3537803E-03 9.6069574E-02 at 140iterations 2.4203584E-03 5.3680420E-02 at 150iterations 1.3538355E-03 2.9104233E-02 at 160iterations 7.5576745E-04 1.6081572E-02 at 170iterations 4.2337010E-04 9.0656281E-03 at 180iterations finished qdiffx linear iterations at : 11:04:07 total time elapsed so far: 14.40000 # loops : 180 mean,max change (kT/e) : 4.2337010E-04 9.0656281E-03 energy calculations done at 14.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.63000 DelPhi exited at 11:04:08 14.627u 0.261s 0:15.23 97.7% 0+0k 0+0io 0pf+0w