Tue Nov 22 14:09:39 PST 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 Nov 22 2011 at 14:09:44 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6351132 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): -10.96400 35.30700 ymin,ymax (A): 1.574000 41.97800 zmin,zma (A): -19.17800 36.87500 x,y,z range (A): 46.27100 40.40400 56.05300 scale (grids/A): 0.6351132 object centre (A): 12.17150 21.77600 8.848500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 89.85706 89.32308 89.98697 assigned negative charge : -284.8263 centred at (gu) : 89.92992 89.44586 89.96956 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5453 nv = 96 ne = 84 npr = 39997 no. pairs analyzed = 39997 no. exposed pairs = 2406 no. arc points = 16739 no. surface atoms = 821 nbur = 1143 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 309 mr = 3142 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1647 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6391 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4214368E-09 5.0088875E-09 midg,1,midg; midg,igrid,midg 1.4818957E-08 -4.8006075E-09 1,midg,midg; igrid,midg,midg 9.4195824E-09 -1.7177894E-09 gauss-seidel spectral radius is 0.9871014 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 14:09:47 rms-change max change #iterations 0.1168763 19.97405 at 10iterations 1.1370819E-02 2.242625 at 20iterations 1.1004586E-03 0.2053280 at 30iterations 1.0673086E-04 2.0232201E-02 at 40iterations 1.0292555E-05 2.0580292E-03 at 50iterations finished qdiffx linear iterations at : 14:09:57 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 1.0292555E-05 2.0580292E-03 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 14:10:00 3.746u 0.208s 0:17.00 23.1% 0+0k 0+0io 3pf+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 Nov 22 2011 at 14:10:02 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.905340 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): -10.96400 35.30700 ymin,ymax (A): 1.574000 41.97800 zmin,zma (A): -19.17800 36.87500 x,y,z range (A): 46.27100 40.40400 56.05300 scale (grids/A): 1.905340 object centre (A): 12.17150 21.77600 8.848500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 89.57104 87.96919 89.96091 assigned negative charge : -284.8263 centred at (gu) : 89.79010 88.33762 89.90887 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 58362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16739 grid for indexing accessible points = 1.400000 m= 22595 mr = 40714 m= 3825 mr = 17592 m= 184 mr = 2605 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 972 time to turn everything in is 0.3100000 number of dielectric boundary points 24002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 14403 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) : 0.6351132 object centre at (A) : 12.17150 21.77600 8.848500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4462605E-02 3.5082314E-02 midg,1,midg; midg,igrid,midg 4.3562595E-03 -7.0383358E-03 1,midg,midg; igrid,midg,midg -3.0884286E-03 -2.2413014E-03 gauss-seidel spectral radius is 0.9985613 estimated iterations to convergence 209 setup time was (sec) 0.5500000 now iterating at: 14:10:07 rms-change max change #iterations 3.551776 174.3282 at 10iterations 1.629865 57.67607 at 20iterations 0.7497979 28.62524 at 30iterations 0.3454931 12.57893 at 40iterations 0.1580315 5.655487 at 50iterations 7.2408736E-02 2.516873 at 60iterations 3.3314433E-02 1.155671 at 70iterations 1.5243219E-02 0.5903511 at 80iterations 7.0071020E-03 0.2419758 at 90iterations 3.2176874E-03 0.1091919 at 100iterations 1.4781201E-03 4.9011230E-02 at 110iterations 6.7837816E-04 2.2732735E-02 at 120iterations finished qdiffx linear iterations at : 14:10:30 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 6.7837816E-04 2.2732735E-02 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.380000 DelPhi exited at 14:10:32 8.384u 0.245s 0:30.64 28.1% 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 Nov 22 2011 at 14:10:34 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.858009 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): -10.96400 35.30700 ymin,ymax (A): 1.574000 41.97800 zmin,zma (A): -19.17800 36.87500 x,y,z range (A): 46.27100 40.40400 56.05300 scale (grids/A): 2.858009 object centre (A): 12.17150 21.77600 8.848500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 89.35665 86.95378 89.94133 assigned negative charge : -284.8263 centred at (gu) : 89.68517 87.50641 89.86338 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 134552 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16739 grid for indexing accessible points = 1.400000 m= 71242 mr = 97951 m= 27973 mr = 59815 m= 7006 mr = 23687 m= 950 mr = 5600 m= 50 mr = 613 m= 0 mr = 29 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 3414 time to turn everything in is 0.8000000 number of dielectric boundary points 54078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 14655 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) : 1.905340 object centre at (A) : 12.17150 21.77600 8.848500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2708973 0.2540202 midg,1,midg; midg,igrid,midg 6.5149076E-04 -8.0451168E-02 1,midg,midg; igrid,midg,midg -6.3428231E-02 -4.8185136E-02 gauss-seidel spectral radius is 0.9992211 estimated iterations to convergence 283 setup time was (sec) 1.070000 now iterating at: 14:10:40 rms-change max change #iterations 8.391311 341.6581 at 10iterations 4.819389 132.8154 at 20iterations 2.737783 101.8267 at 30iterations 1.557866 32.67633 at 40iterations 0.8821972 18.04880 at 50iterations 0.5012407 10.76699 at 60iterations 0.2840178 6.050234 at 70iterations 0.1608087 3.275833 at 80iterations 9.0763412E-02 1.850351 at 90iterations 5.1432833E-02 0.9715064 at 100iterations 2.9043140E-02 0.5909023 at 110iterations 1.6474428E-02 0.3242912 at 120iterations 9.3036052E-03 0.2017244 at 130iterations 5.2579255E-03 0.1165953 at 140iterations 2.9706438E-03 5.8553696E-02 at 150iterations 1.6807592E-03 3.4629822E-02 at 160iterations 9.4954233E-04 1.8049240E-02 at 170iterations 5.3675321E-04 1.1571884E-02 at 180iterations finished qdiffx linear iterations at : 14:11:18 total time elapsed so far: 13.22000 # loops : 180 mean,max change (kT/e) : 5.3675321E-04 1.1571884E-02 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.35000 DelPhi exited at 14:11:19 13.353u 0.235s 0:45.13 30.0% 0+0k 0+0io 0pf+0w