Wed Dec 21 14:21:45 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+sph.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 = amb.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 21 2011 at 14:21:48 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ARG 41 has a net charge of 0.0400 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: 0.6491256 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): -5.095000 34.47700 ymin,ymax (A): -3.459000 48.19700 zmin,zma (A): -24.11900 30.72400 x,y,z range (A): 39.57200 51.65600 54.84300 scale (grids/A): 0.6491256 object centre (A): 14.69100 22.36900 3.302501 number of atom coordinates read : 1954 total number of charged atoms : 1821 net assigned charge : 1.721005 assigned positive charge : 285.0921 centred at (gu) : 90.77207 92.58402 90.04018 assigned negative charge : -283.3713 centred at (gu) : 90.86449 92.76037 90.00909 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5609 nv = 96 ne = 84 npr = 40713 no. pairs analyzed = 40713 no. exposed pairs = 2447 no. arc points = 17252 no. surface atoms = 833 nbur = 1121 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 289 mr = 3112 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2754 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1804 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 6627 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1560739E-10 7.2819533E-09 midg,1,midg; midg,igrid,midg 1.3088968E-08 -2.7494151E-08 1,midg,midg; igrid,midg,midg 1.1673643E-08 -7.3434592E-09 gauss-seidel spectral radius is 0.9876435 estimated iterations to convergence 74 setup time was (sec) 0.6400000 now iterating at: 14:21:50 rms-change max change #iterations 0.1270489 20.63511 at 10iterations 1.3078713E-02 2.329424 at 20iterations 1.3139114E-03 0.2230644 at 30iterations 1.3321548E-04 2.0126343E-02 at 40iterations 1.3586210E-05 2.2506714E-03 at 50iterations finished qdiffx linear iterations at : 14:21:54 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 1.3586210E-05 2.2506714E-03 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 14:22:04 4.421u 0.473s 0:15.62 31.3% 0+0k 0+0io 5pf+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 21 2011 at 14:22:05 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ARG 41 has a net charge of 0.0400 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: 1.947377 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): -5.095000 34.47700 ymin,ymax (A): -3.459000 48.19700 zmin,zma (A): -24.11900 30.72400 x,y,z range (A): 39.57200 51.65600 54.84300 scale (grids/A): 1.947377 object centre (A): 14.69100 22.36900 3.302501 number of atom coordinates read : 1954 total number of charged atoms : 1821 net assigned charge : 1.721005 assigned positive charge : 285.0921 centred at (gu) : 92.31634 97.75198 90.12061 assigned negative charge : -283.3713 centred at (gu) : 92.59382 98.28122 90.02736 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 59923 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17252 grid for indexing accessible points = 1.400000 m= 21730 mr = 41224 m= 3309 mr = 16493 m= 139 mr = 2105 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1043 time to turn everything in is 0.6500000 number of dielectric boundary points 25237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.8300000 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) : 0.6491256 object centre at (A) : 14.69100 22.36900 3.302501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2952787E-02 9.5026400E-03 midg,1,midg; midg,igrid,midg 3.2442536E-02 -1.5993925E-02 1,midg,midg; igrid,midg,midg 6.8774684E-03 -6.3466895E-03 gauss-seidel spectral radius is 0.9986130 estimated iterations to convergence 213 setup time was (sec) 1.040000 now iterating at: 14:22:07 rms-change max change #iterations 3.703064 160.6245 at 10iterations 1.722556 69.11852 at 20iterations 0.8031462 26.64520 at 30iterations 0.3745087 13.46141 at 40iterations 0.1733643 6.081691 at 50iterations 8.0599032E-02 2.786362 at 60iterations 3.7542950E-02 1.361126 at 70iterations 1.7524388E-02 0.5943718 at 80iterations 8.1494320E-03 0.2878590 at 90iterations 3.7647674E-03 0.1191959 at 100iterations 1.7529136E-03 5.7759285E-02 at 110iterations 8.1829075E-04 2.9289246E-02 at 120iterations finished qdiffx linear iterations at : 14:22:19 total time elapsed so far: 13.30000 # loops : 120 mean,max change (kT/e) : 8.1829075E-04 2.9289246E-02 energy calculations done at 13.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.52000 DelPhi exited at 14:22:24 13.523u 0.563s 0:19.31 72.9% 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 Wed Dec 21 2011 at 14:22:25 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ARG 41 has a net charge of 0.0400 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: 2.921066 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): -5.095000 34.47700 ymin,ymax (A): -3.459000 48.19700 zmin,zma (A): -24.11900 30.72400 x,y,z range (A): 39.57200 51.65600 54.84300 scale (grids/A): 2.921066 object centre (A): 14.69100 22.36900 3.302501 number of atom coordinates read : 1954 total number of charged atoms : 1821 net assigned charge : 1.721005 assigned positive charge : 285.0921 centred at (gu) : 93.47449 101.6280 90.18099 assigned negative charge : -283.3713 centred at (gu) : 93.89076 102.4219 90.04108 start vw surface at 0.1400000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 138366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17252 grid for indexing accessible points = 1.400000 m= 70411 mr = 99893 m= 26108 mr = 58204 m= 5917 mr = 21567 m= 619 mr = 4485 m= 23 mr = 397 m= 0 mr = 7 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 3595 time to turn everything in is 1.790000 number of dielectric boundary points 56891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 14568 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) : 1.947377 object centre at (A) : 14.69100 22.36900 3.302501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9827267 -1.3402764E-02 midg,1,midg; midg,igrid,midg 0.3302476 -0.1692727 1,midg,midg; igrid,midg,midg 4.3408100E-02 -4.2716023E-02 gauss-seidel spectral radius is 0.9992405 estimated iterations to convergence 286 setup time was (sec) 2.360000 now iterating at: 14:22:29 rms-change max change #iterations 8.672488 455.4791 at 10iterations 5.010884 143.2767 at 20iterations 2.868284 69.48518 at 30iterations 1.638086 39.65856 at 40iterations 0.9378561 19.18581 at 50iterations 0.5348658 10.61818 at 60iterations 0.3051875 6.347864 at 70iterations 0.1741444 3.250301 at 80iterations 9.9032745E-02 1.992937 at 90iterations 5.6453038E-02 1.173008 at 100iterations 3.2202117E-02 0.7228489 at 110iterations 1.8301347E-02 0.3445466 at 120iterations 1.0416037E-02 0.2186584 at 130iterations 5.9436397E-03 0.1212158 at 140iterations 3.3822453E-03 6.1378479E-02 at 150iterations 1.9215425E-03 3.6743164E-02 at 160iterations 1.0950745E-03 2.0256042E-02 at 170iterations 6.2317657E-04 1.1782050E-02 at 180iterations finished qdiffx linear iterations at : 14:22:50 total time elapsed so far: 22.91000 # loops : 180 mean,max change (kT/e) : 6.2317657E-04 1.1782050E-02 energy calculations done at 22.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.13000 DelPhi exited at 14:22:55 23.134u 0.761s 0:29.82 80.1% 0+0k 0+0io 0pf+0w