Tue Oct 11 03:15:09 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+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 Tue Oct 11 2011 at 03:15:09 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5085 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: 0.4919913 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): 16.07700 85.50900 ymin,ymax (A): 4.961000 68.35500 zmin,zma (A): 2.060000 74.41900 x,y,z range (A): 69.43201 63.39400 72.35900 scale (grids/A): 0.4919913 object centre (A): 50.79300 36.65800 38.23950 number of atom coordinates read : 5085 total number of charged atoms : 4797 net assigned charge : 1.500015 assigned positive charge : 758.6083 centred at (gu) : 91.63200 90.89124 91.48876 assigned negative charge : -757.1142 centred at (gu) : 91.66632 90.80504 91.44068 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7724 nv = 96 ne = 84 npr = 102313 no. pairs analyzed = 102313 no. exposed pairs = 6367 no. arc points = 44951 no. surface atoms = 2117 nbur = 2968 mkacc time = 0.2600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 255 mr = 4004 m= 0 mr = 2 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 0.5200000 number of dielectric boundary points 3973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3983 ## 608 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 10246 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3221117E-11 9.8039854E-11 midg,1,midg; midg,igrid,midg -7.5478977E-11 1.4029675E-10 1,midg,midg; igrid,midg,midg 3.1163305E-11 -5.3168435E-11 gauss-seidel spectral radius is 0.9789066 estimated iterations to convergence 57 setup time was (sec) 0.7800000 now iterating at: 03:15:10 rms-change max change #iterations 6.1397385E-02 11.38830 at 10iterations 3.1390651E-03 0.4631300 at 20iterations 2.6979035E-04 3.7733078E-02 at 30iterations 6.1861218E-05 8.5124969E-03 at 40iterations 1.7079637E-05 2.4038553E-03 at 50iterations finished qdiffx linear iterations at : 03:15:14 total time elapsed so far: 4.980000 # loops : 50 mean,max change (kT/e) : 1.7079637E-05 2.4038553E-03 energy calculations done at 4.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.140000 DelPhi exited at 03:15:15 5.148u 0.396s 0:06.24 88.6% 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 Tue Oct 11 2011 at 03:15:15 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5085 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.475974 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): 16.07700 85.50900 ymin,ymax (A): 4.961000 68.35500 zmin,zma (A): 2.060000 74.41900 x,y,z range (A): 69.43201 63.39400 72.35900 scale (grids/A): 1.475974 object centre (A): 50.79300 36.65800 38.23950 number of atom coordinates read : 5085 total number of charged atoms : 4797 net assigned charge : 1.500015 assigned positive charge : 758.6083 centred at (gu) : 94.89433 92.67214 94.46417 assigned negative charge : -757.1142 centred at (gu) : 94.99850 92.41476 94.32162 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 87591 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44951 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 24559 mr = 59385 m= 1872 mr = 16591 m= 38 mr = 719 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 4822 time to turn everything in is 0.7300000 number of dielectric boundary points 37365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 479 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 35576 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) : 0.4919913 object centre at (A) : 50.79300 36.65800 38.23950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2682369E-03 1.3433136E-02 midg,1,midg; midg,igrid,midg -5.4858681E-03 -1.3537448E-03 1,midg,midg; igrid,midg,midg 2.5924344E-03 -5.9239510E-03 gauss-seidel spectral radius is 0.9979797 estimated iterations to convergence 177 setup time was (sec) 1.100000 now iterating at: 03:15:17 rms-change max change #iterations 3.602034 186.9706 at 10iterations 1.425219 55.26815 at 20iterations 0.5675523 20.52858 at 30iterations 0.2257446 7.757235 at 40iterations 8.9674585E-02 3.017467 at 50iterations 3.5838023E-02 1.081878 at 60iterations 1.4234096E-02 0.5151062 at 70iterations 5.6750863E-03 0.1872807 at 80iterations 2.2816593E-03 7.5042725E-02 at 90iterations 9.2634268E-04 3.0139923E-02 at 100iterations 3.9005675E-04 1.3782263E-02 at 110iterations 1.7496206E-04 6.4854622E-03 at 120iterations finished qdiffx linear iterations at : 03:15:28 total time elapsed so far: 11.92000 # loops : 120 mean,max change (kT/e) : 1.7496206E-04 6.4854622E-03 energy calculations done at 11.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.09000 DelPhi exited at 03:15:28 12.094u 0.447s 0:13.09 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 Tue Oct 11 2011 at 03:15:29 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5085 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.213961 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): 16.07700 85.50900 ymin,ymax (A): 4.961000 68.35500 zmin,zma (A): 2.060000 74.41900 x,y,z range (A): 69.43201 63.39400 72.35900 scale (grids/A): 2.213961 object centre (A): 50.79300 36.65800 38.23950 number of atom coordinates read : 5085 total number of charged atoms : 4797 net assigned charge : 1.500015 assigned positive charge : 758.6083 centred at (gu) : 97.34093 94.00780 96.69585 assigned negative charge : -757.1142 centred at (gu) : 97.49754 93.62208 96.48242 start vw surface at 0.1800000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 204260 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44951 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 89099 mr = 145889 m= 21512 mr = 70105 m= 2565 mr = 15736 m= 75 mr = 1442 m= 0 mr = 10 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 16538 time to turn everything in is 1.750000 number of dielectric boundary points 84329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 38229 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) : 1.475974 object centre at (A) : 50.79300 36.65800 38.23950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5468587E-02 0.1394380 midg,1,midg; midg,igrid,midg -3.8509000E-02 -5.6980986E-02 1,midg,midg; igrid,midg,midg 2.7950283E-02 -0.1671936 gauss-seidel spectral radius is 0.9991254 estimated iterations to convergence 267 setup time was (sec) 2.090000 now iterating at: 03:15:31 rms-change max change #iterations 9.892369 279.0287 at 10iterations 5.548049 136.7000 at 20iterations 3.106736 65.94073 at 30iterations 1.729592 44.75842 at 40iterations 0.9593021 24.48610 at 50iterations 0.5308625 9.718985 at 60iterations 0.2935770 6.102817 at 70iterations 0.1619016 3.336438 at 80iterations 8.9220360E-02 1.855957 at 90iterations 4.9170133E-02 0.9772434 at 100iterations 2.7063442E-02 0.5405502 at 110iterations 1.4876477E-02 0.2954254 at 120iterations 8.1574041E-03 0.1633239 at 130iterations 4.4990084E-03 9.2078209E-02 at 140iterations 2.4728423E-03 5.0860405E-02 at 150iterations 1.3624259E-03 2.6996613E-02 at 160iterations 7.5588183E-04 1.4743805E-02 at 170iterations 4.2294074E-04 8.1024170E-03 at 180iterations finished qdiffx linear iterations at : 03:15:49 total time elapsed so far: 20.07000 # loops : 180 mean,max change (kT/e) : 4.2294074E-04 8.1024170E-03 energy calculations done at 20.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.24000 DelPhi exited at 03:15:50 20.240u 0.476s 0:21.01 98.5% 0+0k 0+0io 0pf+0w