Sat Oct 15 15:45:50 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 Sat Oct 15 2011 at 15:45:50 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2732 !!! WARNING: HIR 43 has a net charge of 0.5140 !!! WARNING: SEP 199 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6618084 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): -8.577000 38.47800 ymin,ymax (A): -26.40700 21.61600 zmin,zma (A): -9.814000 43.97800 x,y,z range (A): 47.05500 48.02300 53.79200 scale (grids/A): 0.6618084 object centre (A): 14.95050 -2.395500 17.08200 number of atom coordinates read : 2732 total number of charged atoms : 2579 net assigned charge : 3.701021 assigned positive charge : 413.8068 centred at (gu) : 90.34656 90.03729 89.05044 assigned negative charge : -410.1064 centred at (gu) : 90.62234 89.84531 89.09556 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7942 nv = 96 ne = 84 npr = 56822 no. pairs analyzed = 56822 no. exposed pairs = 3306 no. arc points = 22551 no. surface atoms = 1110 nbur = 1622 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 467 mr = 4616 m= 6 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.2300000 number of dielectric boundary points 3734 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2222 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9483 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4288088E-08 2.5837141E-10 midg,1,midg; midg,igrid,midg -3.2486767E-08 5.1690357E-08 1,midg,midg; igrid,midg,midg 6.3925448E-08 -5.6042989E-08 gauss-seidel spectral radius is 0.9881719 estimated iterations to convergence 75 setup time was (sec) 0.4100000 now iterating at: 15:45:50 rms-change max change #iterations 0.1777694 22.14200 at 10iterations 1.9594664E-02 2.659340 at 20iterations 2.1540842E-03 0.2706451 at 30iterations 2.7724775E-04 3.5728455E-02 at 40iterations 5.2894553E-05 6.2904358E-03 at 50iterations finished qdiffx linear iterations at : 15:45:53 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 5.2894553E-05 6.2904358E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 15:45:54 3.394u 0.155s 0:03.81 92.9% 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 Sat Oct 15 2011 at 15:45:54 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2732 !!! WARNING: HIR 43 has a net charge of 0.5140 !!! WARNING: SEP 199 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.985425 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): -8.577000 38.47800 ymin,ymax (A): -26.40700 21.61600 zmin,zma (A): -9.814000 43.97800 x,y,z range (A): 47.05500 48.02300 53.79200 scale (grids/A): 1.985425 object centre (A): 14.95050 -2.395500 17.08200 number of atom coordinates read : 2732 total number of charged atoms : 2579 net assigned charge : 3.701021 assigned positive charge : 413.8068 centred at (gu) : 91.03918 90.11166 87.15076 assigned negative charge : -410.1064 centred at (gu) : 91.86665 89.53566 87.28653 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22551 grid for indexing accessible points = 1.400000 m= 32306 mr = 60906 m= 5437 mr = 24368 m= 347 mr = 3525 m= 1 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1950 time to turn everything in is 0.4100000 number of dielectric boundary points 34426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20379 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) : 0.6618084 object centre at (A) : 14.95050 -2.395500 17.08200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5648248E-03 -1.2584597E-02 midg,1,midg; midg,igrid,midg -2.5065048E-02 4.1722603E-02 1,midg,midg; igrid,midg,midg 6.8498358E-02 -1.5388366E-03 gauss-seidel spectral radius is 0.9987490 estimated iterations to convergence 224 setup time was (sec) 0.6300000 now iterating at: 15:45:55 rms-change max change #iterations 4.809218 224.2316 at 10iterations 2.340062 72.70384 at 20iterations 1.129972 34.92603 at 30iterations 0.5486264 18.87324 at 40iterations 0.2661399 7.457414 at 50iterations 0.1290822 3.816867 at 60iterations 6.2370483E-02 1.821098 at 70iterations 3.0286890E-02 0.9281235 at 80iterations 1.4674899E-02 0.4204776 at 90iterations 7.1299179E-03 0.2090149 at 100iterations 3.4688027E-03 0.1190567 at 110iterations 1.6970371E-03 4.9014568E-02 at 120iterations finished qdiffx linear iterations at : 15:46:02 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 1.6970371E-03 4.9014568E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 15:46:02 7.843u 0.192s 0:08.39 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 Sat Oct 15 2011 at 15:46:02 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2732 !!! WARNING: HIR 43 has a net charge of 0.5140 !!! WARNING: SEP 199 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.978138 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): -8.577000 38.47800 ymin,ymax (A): -26.40700 21.61600 zmin,zma (A): -9.814000 43.97800 x,y,z range (A): 47.05500 48.02300 53.79200 scale (grids/A): 2.978138 object centre (A): 14.95050 -2.395500 17.08200 number of atom coordinates read : 2732 total number of charged atoms : 2579 net assigned charge : 3.701021 assigned positive charge : 413.8068 centred at (gu) : 91.55849 90.16748 85.72603 assigned negative charge : -410.1064 centred at (gu) : 92.79992 89.30334 85.92973 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 197195 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22551 grid for indexing accessible points = 1.400000 m= 103511 mr = 146836 m= 38909 mr = 86133 m= 9652 mr = 31688 m= 1471 mr = 7374 m= 102 mr = 1069 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 6380 time to turn everything in is 1.090000 number of dielectric boundary points 77679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 20620 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) : 1.985425 object centre at (A) : 14.95050 -2.395500 17.08200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3298227 -0.1452083 midg,1,midg; midg,igrid,midg -0.2734624 0.4320827 1,midg,midg; igrid,midg,midg 0.6057767 7.8968361E-02 gauss-seidel spectral radius is 0.9992855 estimated iterations to convergence 295 setup time was (sec) 1.330000 now iterating at: 15:46:04 rms-change max change #iterations 10.95254 345.6586 at 10iterations 6.456489 174.5499 at 20iterations 3.794355 72.04402 at 30iterations 2.224986 41.52723 at 40iterations 1.302855 25.20095 at 50iterations 0.7615353 13.56156 at 60iterations 0.4440029 7.790661 at 70iterations 0.2590677 4.474685 at 80iterations 0.1509610 2.688473 at 90iterations 8.7760553E-02 1.418346 at 100iterations 5.1292323E-02 0.9564085 at 110iterations 2.9862925E-02 0.5299835 at 120iterations 1.7417481E-02 0.2974997 at 130iterations 1.0158205E-02 0.1687441 at 140iterations 5.9630051E-03 0.1011016 at 150iterations 3.5123152E-03 5.4384232E-02 at 160iterations 2.0920162E-03 3.6874771E-02 at 170iterations 1.2666250E-03 2.1902084E-02 at 180iterations finished qdiffx linear iterations at : 15:46:15 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 1.2666250E-03 2.1902084E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 15:46:16 12.842u 0.202s 0:13.40 97.3% 0+0k 0+0io 0pf+0w