Mon Oct 10 11:56:09 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 11:56:09 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7586089 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): 9.252001 56.18000 ymin,ymax (A): -9.211000 36.46700 zmin,zma (A): -3.023000 43.57200 x,y,z range (A): 46.92800 45.67800 46.59500 scale (grids/A): 0.7586089 object centre (A): 32.71600 13.62800 20.27450 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.371980 assigned positive charge : 320.1998 centred at (gu) : 89.28760 90.56194 90.14172 assigned negative charge : -326.5720 centred at (gu) : 89.28230 90.63833 90.34571 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8506 nv = 96 ne = 84 npr = 43339 no. pairs analyzed = 43339 no. exposed pairs = 2721 no. arc points = 19176 no. surface atoms = 914 nbur = 1203 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 599 mr = 4735 m= 8 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 98 time to turn everything in is 0.2700000 number of dielectric boundary points 4237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1529 ## 120 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8793 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3172264E-07 -4.8933038E-07 midg,1,midg; midg,igrid,midg -4.6843326E-08 -3.1025027E-07 1,midg,midg; igrid,midg,midg -1.9591413E-07 -1.3844932E-07 gauss-seidel spectral radius is 0.9909446 estimated iterations to convergence 85 setup time was (sec) 0.5400000 now iterating at: 11:56:10 rms-change max change #iterations 0.2728310 43.77412 at 10iterations 3.9033290E-02 5.564995 at 20iterations 5.4857163E-03 0.7831860 at 30iterations 7.6383498E-04 9.3651772E-02 at 40iterations 1.0927120E-04 1.6990662E-02 at 50iterations finished qdiffx linear iterations at : 11:56:14 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 1.0927120E-04 1.6990662E-02 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 11:56:14 4.566u 0.399s 0:05.27 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 Mon Oct 10 2011 at 11:56:14 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.275827 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): 9.252001 56.18000 ymin,ymax (A): -9.211000 36.46700 zmin,zma (A): -3.023000 43.57200 x,y,z range (A): 46.92800 45.67800 46.59500 scale (grids/A): 2.275827 object centre (A): 32.71600 13.62800 20.27450 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.371980 assigned positive charge : 320.1998 centred at (gu) : 87.86277 91.68562 90.42497 assigned negative charge : -326.5720 centred at (gu) : 87.84674 91.91490 91.03710 start vw surface at 0.1000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 88741 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19176 grid for indexing accessible points = 1.400000 m= 35961 mr = 61393 m= 8205 mr = 27450 m= 992 mr = 5778 m= 39 mr = 562 m= 0 mr = 8 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 2494 time to turn everything in is 0.7300000 number of dielectric boundary points 38747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15753 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) : 0.7586089 object centre at (A) : 32.71600 13.62800 20.27450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5537696E-03 -0.1415434 midg,1,midg; midg,igrid,midg -3.5227384E-02 -5.1999398E-02 1,midg,midg; igrid,midg,midg -1.6837714E-03 1.1277195E-02 gauss-seidel spectral radius is 0.9989706 estimated iterations to convergence 246 setup time was (sec) 1.030000 now iterating at: 11:56:16 rms-change max change #iterations 5.419936 215.8465 at 10iterations 2.791288 86.86292 at 20iterations 1.442859 43.63593 at 30iterations 0.7423247 20.27058 at 40iterations 0.3852210 10.24169 at 50iterations 0.1990486 5.607222 at 60iterations 0.1032729 3.074885 at 70iterations 5.3212397E-02 1.529875 at 80iterations 2.7561180E-02 0.7463014 at 90iterations 1.4305050E-02 0.4338646 at 100iterations 7.3705823E-03 0.2062187 at 110iterations 3.8115147E-03 0.1088524 at 120iterations finished qdiffx linear iterations at : 11:56:26 total time elapsed so far: 11.35000 # loops : 120 mean,max change (kT/e) : 3.8115147E-03 0.1088524 energy calculations done at 11.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.50000 DelPhi exited at 11:56:27 11.509u 0.469s 0:12.41 96.3% 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 Mon Oct 10 2011 at 11:56:27 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.413740 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): 9.252001 56.18000 ymin,ymax (A): -9.211000 36.46700 zmin,zma (A): -3.023000 43.57200 x,y,z range (A): 46.92800 45.67800 46.59500 scale (grids/A): 3.413740 object centre (A): 32.71600 13.62800 20.27450 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.371980 assigned positive charge : 320.1998 centred at (gu) : 86.79405 92.52833 90.63746 assigned negative charge : -326.5720 centred at (gu) : 86.77011 92.87238 91.55571 start vw surface at 0.1000000 fill in re-entrant regions at 0.9300000 boundary points on vw surface= 204278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19176 grid for indexing accessible points = 1.400000 m= 109644 mr = 147826 m= 47880 mr = 91323 m= 15799 mr = 39784 m= 3995 mr = 12637 m= 611 mr = 3095 m= 33 mr = 404 m= 0 mr = 11 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 8446 time to turn everything in is 2.350000 number of dielectric boundary points 87160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.500000 number of grid points assigned charge 15824 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) : 2.275827 object centre at (A) : 32.71600 13.62800 20.27450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1620317 -1.310145 midg,1,midg; midg,igrid,midg -0.2847958 -0.2291707 1,midg,midg; igrid,midg,midg -3.6475367E-03 9.2496285E-03 gauss-seidel spectral radius is 0.9993293 estimated iterations to convergence 305 setup time was (sec) 2.720000 now iterating at: 11:56:30 rms-change max change #iterations 11.48018 269.0540 at 10iterations 6.803698 143.9586 at 20iterations 4.024388 68.34790 at 30iterations 2.383893 38.68940 at 40iterations 1.404432 22.98189 at 50iterations 0.8296401 13.78908 at 60iterations 0.4894352 8.078363 at 70iterations 0.2892559 4.611090 at 80iterations 0.1708202 2.731423 at 90iterations 0.1007265 1.604446 at 100iterations 5.9351590E-02 0.8921789 at 110iterations 3.5035335E-02 0.5555115 at 120iterations 2.0652555E-02 0.3599067 at 130iterations 1.2182320E-02 0.1876135 at 140iterations 7.1920399E-03 0.1113580 at 150iterations 4.2444556E-03 6.7588806E-02 at 160iterations 2.5056710E-03 3.6392212E-02 at 170iterations 1.4781472E-03 2.3126245E-02 at 180iterations finished qdiffx linear iterations at : 11:56:47 total time elapsed so far: 19.67000 # loops : 180 mean,max change (kT/e) : 1.4781472E-03 2.3126245E-02 energy calculations done at 19.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.83000 DelPhi exited at 11:56:47 19.838u 0.457s 0:20.63 98.3% 0+0k 0+0io 0pf+0w