Mon Oct 10 09:26:16 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 09:26:16 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 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: 0.6468964 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): -3.645000 48.69200 ymin,ymax (A): -5.155000 34.31400 zmin,zma (A): -23.74600 31.28600 x,y,z range (A): 52.33700 39.46900 55.03200 scale (grids/A): 0.6468964 object centre (A): 22.52350 14.57950 3.770000 number of atom coordinates read : 1954 total number of charged atoms : 1822 net assigned charge : 5.000010 assigned positive charge : 290.5620 centred at (gu) : 92.31989 89.57280 89.95200 assigned negative charge : -285.5623 centred at (gu) : 92.41213 89.48899 89.89973 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5579 nv = 96 ne = 84 npr = 40184 no. pairs analyzed = 40184 no. exposed pairs = 2529 no. arc points = 17531 no. surface atoms = 864 nbur = 1090 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 263 mr = 3034 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1774 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6545 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7417105E-09 1.4296470E-08 midg,1,midg; midg,igrid,midg 4.1241360E-10 1.6121598E-08 1,midg,midg; igrid,midg,midg 1.1419408E-08 -1.1809740E-09 gauss-seidel spectral radius is 0.9875619 estimated iterations to convergence 73 setup time was (sec) 0.4600000 now iterating at: 09:26:17 rms-change max change #iterations 0.1330490 22.58591 at 10iterations 1.3287713E-02 2.182369 at 20iterations 1.3393608E-03 0.2161922 at 30iterations 1.3660536E-04 2.4211884E-02 at 40iterations 1.3801690E-05 2.1057129E-03 at 50iterations finished qdiffx linear iterations at : 09:26:20 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 1.3801690E-05 2.1057129E-03 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 09:26:20 3.283u 0.237s 0:03.92 89.5% 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 09:26:20 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 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: 1.940689 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): -3.645000 48.69200 ymin,ymax (A): -5.155000 34.31400 zmin,zma (A): -23.74600 31.28600 x,y,z range (A): 52.33700 39.46900 55.03200 scale (grids/A): 1.940689 object centre (A): 22.52350 14.57950 3.770000 number of atom coordinates read : 1954 total number of charged atoms : 1822 net assigned charge : 5.000010 assigned positive charge : 290.5620 centred at (gu) : 96.95984 88.71852 89.85594 assigned negative charge : -285.5623 centred at (gu) : 97.23640 88.46712 89.69915 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 59794 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17531 grid for indexing accessible points = 1.400000 m= 21385 mr = 40682 m= 3078 mr = 16113 m= 146 mr = 1931 m= 0 mr = 54 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 25623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 14386 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) : 0.6468964 object centre at (A) : 22.52350 14.57950 3.770000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8640806E-02 1.2597884E-02 midg,1,midg; midg,igrid,midg 6.1454047E-03 7.8575891E-03 1,midg,midg; igrid,midg,midg 3.2063723E-02 2.2000919E-05 gauss-seidel spectral radius is 0.9986070 estimated iterations to convergence 212 setup time was (sec) 0.7400000 now iterating at: 09:26:21 rms-change max change #iterations 3.710920 168.3422 at 10iterations 1.721840 85.27397 at 20iterations 0.8007504 28.99886 at 30iterations 0.3728650 13.16370 at 40iterations 0.1726561 5.706651 at 50iterations 8.0279678E-02 2.709244 at 60iterations 3.7155356E-02 1.362091 at 70iterations 1.7302606E-02 0.5996933 at 80iterations 8.0468114E-03 0.2881207 at 90iterations 3.7298696E-03 0.1296844 at 100iterations 1.7296801E-03 5.7914734E-02 at 110iterations 8.0357096E-04 2.7931690E-02 at 120iterations finished qdiffx linear iterations at : 09:26:28 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 8.0357096E-04 2.7931690E-02 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.450000 DelPhi exited at 09:26:28 7.449u 0.214s 0:08.00 95.6% 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 09:26:28 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 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: 2.911033 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): -3.645000 48.69200 ymin,ymax (A): -5.155000 34.31400 zmin,zma (A): -23.74600 31.28600 x,y,z range (A): 52.33700 39.46900 55.03200 scale (grids/A): 2.911033 object centre (A): 22.52350 14.57950 3.770000 number of atom coordinates read : 1954 total number of charged atoms : 1822 net assigned charge : 5.000010 assigned positive charge : 290.5620 centred at (gu) : 100.4399 88.07790 89.78387 assigned negative charge : -285.5623 centred at (gu) : 100.8547 87.70078 89.54883 start vw surface at 0.1300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 138089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17531 grid for indexing accessible points = 1.400000 m= 69146 mr = 98555 m= 24860 mr = 56904 m= 5413 mr = 20351 m= 659 mr = 4160 m= 31 mr = 437 m= 0 mr = 15 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.070000 number of dielectric boundary points 57776 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 14576 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) : 1.940689 object centre at (A) : 22.52350 14.57950 3.770000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9177382 8.9134397E-03 midg,1,midg; midg,igrid,midg 0.1283118 4.7721487E-02 1,midg,midg; igrid,midg,midg 0.2839116 -7.7454358E-02 gauss-seidel spectral radius is 0.9992393 estimated iterations to convergence 286 setup time was (sec) 1.370000 now iterating at: 09:26:30 rms-change max change #iterations 8.765607 432.9950 at 10iterations 5.065845 155.3683 at 20iterations 2.905858 73.03629 at 30iterations 1.660970 35.09194 at 40iterations 0.9486526 24.08741 at 50iterations 0.5421845 10.39336 at 60iterations 0.3092999 5.967931 at 70iterations 0.1762681 3.749256 at 80iterations 0.1002397 1.985605 at 90iterations 5.7000861E-02 1.197605 at 100iterations 3.2487202E-02 0.6610761 at 110iterations 1.8460359E-02 0.3959198 at 120iterations 1.0547035E-02 0.2165403 at 130iterations 5.9848805E-03 0.1125364 at 140iterations 3.4030562E-03 6.6444397E-02 at 150iterations 1.9385000E-03 3.8228989E-02 at 160iterations 1.0992950E-03 2.0732880E-02 at 170iterations 6.2660256E-04 1.1466980E-02 at 180iterations finished qdiffx linear iterations at : 09:26:40 total time elapsed so far: 11.56000 # loops : 180 mean,max change (kT/e) : 6.2660256E-04 1.1466980E-02 energy calculations done at 11.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.74000 DelPhi exited at 09:26:41 11.740u 0.225s 0:12.23 97.7% 0+0k 0+0io 0pf+0w