Mon Oct 10 13:55:11 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+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 Mon Oct 10 2011 at 13:55:11 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7377933 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): -21.75700 24.60800 ymin,ymax (A): -7.231000 36.18100 zmin,zma (A): -3.552000 44.70000 x,y,z range (A): 46.36500 43.41200 48.25200 scale (grids/A): 0.7377933 object centre (A): 1.425500 14.47500 20.57400 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 89.17675 90.24919 90.07822 assigned negative charge : -323.3720 centred at (gu) : 89.20666 90.32439 90.26389 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7950 nv = 96 ne = 84 npr = 43617 no. pairs analyzed = 43617 no. exposed pairs = 2713 no. arc points = 19081 no. surface atoms = 913 nbur = 1204 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 573 mr = 4436 m= 2 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 75 time to turn everything in is 0.2900000 number of dielectric boundary points 3959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1528 ## 126 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8361 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2680955E-08 -2.9473841E-07 midg,1,midg; midg,igrid,midg -3.0596659E-08 -1.8781566E-07 1,midg,midg; igrid,midg,midg -8.7636046E-08 -1.1570232E-07 gauss-seidel spectral radius is 0.9904286 estimated iterations to convergence 83 setup time was (sec) 0.5500000 now iterating at: 13:55:11 rms-change max change #iterations 0.2484906 32.56783 at 10iterations 3.2992251E-02 4.072045 at 20iterations 4.3961043E-03 0.5838013 at 30iterations 5.9672265E-04 7.1098328E-02 at 40iterations 7.9447302E-05 1.0702133E-02 at 50iterations finished qdiffx linear iterations at : 13:55:14 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 7.9447302E-05 1.0702133E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 13:55:15 3.494u 0.162s 0:04.36 83.7% 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 Mon Oct 10 2011 at 13:55:15 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.213380 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): -21.75700 24.60800 ymin,ymax (A): -7.231000 36.18100 zmin,zma (A): -3.552000 44.70000 x,y,z range (A): 46.36500 43.41200 48.25200 scale (grids/A): 2.213380 object centre (A): 1.425500 14.47500 20.57400 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 87.53023 90.74779 90.23464 assigned negative charge : -323.3720 centred at (gu) : 87.61986 90.97313 90.79160 start vw surface at 0.1900000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 82912 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19081 grid for indexing accessible points = 1.400000 m= 34041 mr = 57065 m= 7220 mr = 26063 m= 668 mr = 5006 m= 20 mr = 359 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 2189 time to turn everything in is 0.7500000 number of dielectric boundary points 36367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 15756 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) : 0.7377933 object centre at (A) : 1.425500 14.47500 20.57400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8636556E-03 -0.1373089 midg,1,midg; midg,igrid,midg -2.5038481E-02 -3.0424153E-02 1,midg,midg; igrid,midg,midg -1.5870625E-03 -9.6877357E-03 gauss-seidel spectral radius is 0.9989219 estimated iterations to convergence 241 setup time was (sec) 1.050000 now iterating at: 13:55:16 rms-change max change #iterations 5.062829 202.3622 at 10iterations 2.560407 81.12738 at 20iterations 1.304121 41.26955 at 30iterations 0.6629424 18.49346 at 40iterations 0.3370264 10.22181 at 50iterations 0.1716099 5.483025 at 60iterations 8.7412782E-02 2.301073 at 70iterations 4.4363845E-02 1.302034 at 80iterations 2.2669470E-02 0.6733093 at 90iterations 1.1517802E-02 0.3354330 at 100iterations 5.8689700E-03 0.1801434 at 110iterations 2.9984349E-03 8.1428528E-02 at 120iterations finished qdiffx linear iterations at : 13:55:23 total time elapsed so far: 8.160000 # loops : 120 mean,max change (kT/e) : 2.9984349E-03 8.1428528E-02 energy calculations done at 8.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.350000 DelPhi exited at 13:55:24 8.350u 0.233s 0:08.88 96.6% 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 13:55:24 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.320070 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): -21.75700 24.60800 ymin,ymax (A): -7.231000 36.18100 zmin,zma (A): -3.552000 44.70000 x,y,z range (A): 46.36500 43.41200 48.25200 scale (grids/A): 3.320070 object centre (A): 1.425500 14.47500 20.57400 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 86.29520 91.12162 90.35197 assigned negative charge : -323.3720 centred at (gu) : 86.42979 91.45975 91.18745 start vw surface at 0.1400000 fill in re-entrant regions at 0.9600000 boundary points on vw surface= 190468 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19081 grid for indexing accessible points = 1.400000 m= 103043 mr = 137079 m= 45064 mr = 85567 m= 13717 mr = 37581 m= 2817 mr = 10859 m= 313 mr = 2137 m= 10 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 7356 time to turn everything in is 2.130000 number of dielectric boundary points 82031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.290000 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) : 2.213380 object centre at (A) : 1.425500 14.47500 20.57400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1040924 -1.307581 midg,1,midg; midg,igrid,midg -0.2337341 -0.1430610 1,midg,midg; igrid,midg,midg 5.8967382E-02 -0.1991721 gauss-seidel spectral radius is 0.9993165 estimated iterations to convergence 302 setup time was (sec) 2.480000 now iterating at: 13:55:27 rms-change max change #iterations 10.95093 272.0637 at 10iterations 6.442651 123.2743 at 20iterations 3.804388 100.2002 at 30iterations 2.241012 39.67053 at 40iterations 1.316612 24.25671 at 50iterations 0.7756999 13.50391 at 60iterations 0.4547494 7.839279 at 70iterations 0.2678187 4.274739 at 80iterations 0.1570676 2.790233 at 90iterations 9.2080139E-02 1.500847 at 100iterations 5.4197777E-02 0.9496908 at 110iterations 3.1794883E-02 0.5158692 at 120iterations 1.8710328E-02 0.3261490 at 130iterations 1.0931939E-02 0.1851935 at 140iterations 6.4375531E-03 0.1001129 at 150iterations 3.7663479E-03 6.0519755E-02 at 160iterations 2.2123922E-03 4.0100098E-02 at 170iterations 1.2977876E-03 2.0565033E-02 at 180iterations finished qdiffx linear iterations at : 13:55:38 total time elapsed so far: 14.02000 # loops : 180 mean,max change (kT/e) : 1.2977876E-03 2.0565033E-02 energy calculations done at 14.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.22000 DelPhi exited at 13:55:39 14.222u 0.260s 0:15.03 96.3% 0+0k 0+0io 0pf+0w