Sun Oct 9 22:33:57 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 Sun Oct 9 2011 at 22:33:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3153 !!! WARNING: CYS 260 has a net charge of 0.5000 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: 0.6688837 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): 45.47100 98.69400 ymin,ymax (A): 2.919000 55.22400 zmin,zma (A): 15.32000 67.89300 x,y,z range (A): 53.22300 52.30500 52.57300 scale (grids/A): 0.6688837 object centre (A): 72.08250 29.07150 41.60650 number of atom coordinates read : 3153 total number of charged atoms : 3006 net assigned charge : 7.000022 assigned positive charge : 477.0919 centred at (gu) : 90.39812 88.96098 90.52402 assigned negative charge : -470.0931 centred at (gu) : 90.27219 88.87009 90.46149 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 9670 nv = 96 ne = 84 npr = 61999 no. pairs analyzed = 61999 no. exposed pairs = 4043 no. arc points = 28793 no. surface atoms = 1349 nbur = 1804 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 620 mr = 5302 m= 4 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 78 time to turn everything in is 0.2400000 number of dielectric boundary points 4885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2720 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 11321 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4880798E-09 4.5882434E-08 midg,1,midg; midg,igrid,midg -6.4357719E-09 4.0154376E-08 1,midg,midg; igrid,midg,midg -1.4276103E-08 6.4968390E-08 gauss-seidel spectral radius is 0.9884732 estimated iterations to convergence 76 setup time was (sec) 0.4300000 now iterating at: 22:33:58 rms-change max change #iterations 0.1970154 24.82851 at 10iterations 2.1350779E-02 2.813934 at 20iterations 2.3460353E-03 0.2842522 at 30iterations 2.6100682E-04 2.9201508E-02 at 40iterations 2.8845583E-05 3.7631989E-03 at 50iterations finished qdiffx linear iterations at : 22:34:01 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 2.8845583E-05 3.7631989E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 22:34:02 3.488u 0.175s 0:04.03 90.5% 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 Sun Oct 9 2011 at 22:34:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3153 !!! WARNING: CYS 260 has a net charge of 0.5000 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: 2.006651 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): 45.47100 98.69400 ymin,ymax (A): 2.919000 55.22400 zmin,zma (A): 15.32000 67.89300 x,y,z range (A): 53.22300 52.30500 52.57300 scale (grids/A): 2.006651 object centre (A): 72.08250 29.07150 41.60650 number of atom coordinates read : 3153 total number of charged atoms : 3006 net assigned charge : 7.000022 assigned positive charge : 477.0919 centred at (gu) : 91.19336 86.88171 91.57166 assigned negative charge : -470.0931 centred at (gu) : 90.81653 86.61005 91.38421 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 103991 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28793 grid for indexing accessible points = 1.400000 m= 38367 mr = 71980 m= 7052 mr = 28170 m= 637 mr = 4569 m= 11 mr = 344 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 3196 time to turn everything in is 0.5100000 number of dielectric boundary points 44995 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 23742 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) : 0.6688837 object centre at (A) : 72.08250 29.07150 41.60650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7134710E-03 2.2742959E-02 midg,1,midg; midg,igrid,midg 3.9987393E-02 4.4637740E-02 1,midg,midg; igrid,midg,midg 3.9422843E-03 2.9161468E-02 gauss-seidel spectral radius is 0.9988264 estimated iterations to convergence 231 setup time was (sec) 0.7300000 now iterating at: 22:34:03 rms-change max change #iterations 5.255288 216.2773 at 10iterations 2.602118 77.28329 at 20iterations 1.279868 33.34580 at 30iterations 0.6314933 18.37208 at 40iterations 0.3132626 8.515085 at 50iterations 0.1544257 4.193788 at 60iterations 7.6826483E-02 1.939928 at 70iterations 3.7769109E-02 1.088900 at 80iterations 1.8707935E-02 0.5178595 at 90iterations 9.2650698E-03 0.2674370 at 100iterations 4.5844386E-03 0.1198044 at 110iterations 2.2619641E-03 5.9440613E-02 at 120iterations finished qdiffx linear iterations at : 22:34:10 total time elapsed so far: 8.080000 # loops : 120 mean,max change (kT/e) : 2.2619641E-03 5.9440613E-02 energy calculations done at 8.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.220000 DelPhi exited at 22:34:10 8.222u 0.210s 0:08.72 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 Sun Oct 9 2011 at 22:34:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3153 !!! WARNING: CYS 260 has a net charge of 0.5000 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: 3.009977 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): 45.47100 98.69400 ymin,ymax (A): 2.919000 55.22400 zmin,zma (A): 15.32000 67.89300 x,y,z range (A): 53.22300 52.30500 52.57300 scale (grids/A): 3.009977 object centre (A): 72.08250 29.07150 41.60650 number of atom coordinates read : 3153 total number of charged atoms : 3006 net assigned charge : 7.000022 assigned positive charge : 477.0919 centred at (gu) : 91.78965 85.32236 92.35738 assigned negative charge : -470.0931 centred at (gu) : 91.22472 84.91502 92.07623 start vw surface at 0.1100000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 240313 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28793 grid for indexing accessible points = 1.400000 m= 122759 mr = 174326 m= 46378 mr = 100332 m= 13013 mr = 37086 m= 2596 mr = 9919 m= 304 mr = 2001 m= 5 mr = 196 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 10612 time to turn everything in is 1.330000 number of dielectric boundary points 101508 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 24048 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) : 2.006651 object centre at (A) : 72.08250 29.07150 41.60650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9992471E-03 -1.6666525E-04 midg,1,midg; midg,igrid,midg 0.2586749 0.2963248 1,midg,midg; igrid,midg,midg 0.2326477 0.2971714 gauss-seidel spectral radius is 0.9993290 estimated iterations to convergence 305 setup time was (sec) 1.600000 now iterating at: 22:34:12 rms-change max change #iterations 12.05126 366.8051 at 10iterations 7.253787 180.4857 at 20iterations 4.355087 112.1215 at 30iterations 2.611835 52.22365 at 40iterations 1.560256 27.02538 at 50iterations 0.9306819 17.27217 at 60iterations 0.5526870 10.02504 at 70iterations 0.3290125 5.773075 at 80iterations 0.1953090 3.481802 at 90iterations 0.1160886 2.053947 at 100iterations 6.8759069E-02 1.211760 at 110iterations 4.0704064E-02 0.6484613 at 120iterations 2.4039049E-02 0.4321976 at 130iterations 1.4254760E-02 0.2226925 at 140iterations 8.4184809E-03 0.1355267 at 150iterations 4.9877586E-03 7.7110291E-02 at 160iterations 2.9513324E-03 4.8788071E-02 at 170iterations 1.7451938E-03 2.7748108E-02 at 180iterations finished qdiffx linear iterations at : 22:34:24 total time elapsed so far: 13.62000 # loops : 180 mean,max change (kT/e) : 1.7451938E-03 2.7748108E-02 energy calculations done at 13.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.76000 DelPhi exited at 22:34:25 13.757u 0.189s 0:14.29 97.4% 0+0k 0+0io 0pf+0w