Sat Oct 15 11:26:23 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 Sat Oct 15 2011 at 11:26:23 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2580 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 0.6266613 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): -31.71200 17.51600 ymin,ymax (A): -23.52600 22.86800 zmin,zma (A): -11.62800 45.18100 x,y,z range (A): 49.22800 46.39400 56.80900 scale (grids/A): 0.6266613 object centre (A): -7.098000 -0.3289995 16.77650 number of atom coordinates read : 2580 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.41229 89.22369 89.40366 assigned negative charge : -387.4045 centred at (gu) : 88.30443 89.26434 89.29346 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6525 nv = 96 ne = 84 npr = 53685 no. pairs analyzed = 53685 no. exposed pairs = 2954 no. arc points = 20892 no. surface atoms = 1000 nbur = 1580 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3664 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 117 time to turn everything in is 0.2000000 number of dielectric boundary points 3150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2092 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8108 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5231708E-09 1.1266911E-08 midg,1,midg; midg,igrid,midg 8.7093452E-09 7.4884898E-10 1,midg,midg; igrid,midg,midg -6.7016779E-09 8.9681933E-09 gauss-seidel spectral radius is 0.9868031 estimated iterations to convergence 71 setup time was (sec) 0.4800000 now iterating at: 11:26:24 rms-change max change #iterations 0.1334716 21.71918 at 10iterations 1.2650006E-02 1.514915 at 20iterations 1.2039115E-03 0.1614971 at 30iterations 1.1261094E-04 1.9119263E-02 at 40iterations 1.0739699E-05 1.5935898E-03 at 50iterations finished qdiffx linear iterations at : 11:26:28 total time elapsed so far: 4.220000 # loops : 50 mean,max change (kT/e) : 1.0739699E-05 1.5935898E-03 energy calculations done at 4.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.360000 DelPhi exited at 11:26:28 4.359u 0.309s 0:05.19 89.5% 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 Sat Oct 15 2011 at 11:26:29 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2580 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 1.879984 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): -31.71200 17.51600 ymin,ymax (A): -23.52600 22.86800 zmin,zma (A): -11.62800 45.18100 x,y,z range (A): 49.22800 46.39400 56.80900 scale (grids/A): 1.879984 object centre (A): -7.098000 -0.3289995 16.77650 number of atom coordinates read : 2580 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.23602 87.67068 88.21075 assigned negative charge : -387.4045 centred at (gu) : 84.91331 87.79285 87.88005 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20892 grid for indexing accessible points = 1.400000 m= 25174 mr = 50350 m= 3675 mr = 18942 m= 199 mr = 2287 m= 2 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 5902 time to turn everything in is 0.3800000 number of dielectric boundary points 28869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 19243 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) : 0.6266613 object centre at (A) : -7.098000 -0.3289995 16.77650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7118817E-02 2.6654039E-02 midg,1,midg; midg,igrid,midg 1.1856897E-02 1.4086530E-03 1,midg,midg; igrid,midg,midg -8.4078535E-03 3.2956373E-02 gauss-seidel spectral radius is 0.9985909 estimated iterations to convergence 211 setup time was (sec) 0.7100000 now iterating at: 11:26:30 rms-change max change #iterations 4.106386 163.0395 at 10iterations 1.900920 62.52887 at 20iterations 0.8811376 29.17240 at 30iterations 0.4070197 14.16994 at 40iterations 0.1888075 5.834536 at 50iterations 8.7223157E-02 2.919401 at 60iterations 4.0501039E-02 1.302568 at 70iterations 1.8715179E-02 0.6360989 at 80iterations 8.6683277E-03 0.2662220 at 90iterations 4.0165628E-03 0.1398883 at 100iterations 1.8581084E-03 5.6022644E-02 at 110iterations 8.6062454E-04 2.8251648E-02 at 120iterations finished qdiffx linear iterations at : 11:26:39 total time elapsed so far: 10.25000 # loops : 120 mean,max change (kT/e) : 8.6062454E-04 2.8251648E-02 energy calculations done at 10.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.38000 DelPhi exited at 11:26:40 10.385u 0.340s 0:11.97 89.5% 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 Sat Oct 15 2011 at 11:26:41 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2580 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 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: 2.819976 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): -31.71200 17.51600 ymin,ymax (A): -23.52600 22.86800 zmin,zma (A): -11.62800 45.18100 x,y,z range (A): 49.22800 46.39400 56.80900 scale (grids/A): 2.819976 object centre (A): -7.098000 -0.3289995 16.77650 number of atom coordinates read : 2580 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 82.85400 86.50575 87.31602 assigned negative charge : -387.4045 centred at (gu) : 82.36989 86.68935 86.82008 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 165520 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20892 grid for indexing accessible points = 1.400000 m= 83378 mr = 121627 m= 28637 mr = 69241 m= 6508 mr = 23391 m= 867 mr = 4933 m= 64 mr = 569 m= 5 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 19908 time to turn everything in is 0.9600000 number of dielectric boundary points 65183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 19628 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) : 1.879984 object centre at (A) : -7.098000 -0.3289995 16.77650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6242065E-02 0.3131101 midg,1,midg; midg,igrid,midg 0.1491984 -2.0013847E-03 1,midg,midg; igrid,midg,midg -7.9910971E-02 0.4318757 gauss-seidel spectral radius is 0.9992397 estimated iterations to convergence 286 setup time was (sec) 1.270000 now iterating at: 11:26:42 rms-change max change #iterations 9.562940 290.8732 at 10iterations 5.472362 109.7204 at 20iterations 3.113488 60.81699 at 30iterations 1.773384 33.62431 at 40iterations 1.010772 18.35696 at 50iterations 0.5755407 10.37709 at 60iterations 0.3275564 6.409976 at 70iterations 0.1865904 3.438782 at 80iterations 0.1059597 1.948853 at 90iterations 6.0465101E-02 1.216894 at 100iterations 3.4410045E-02 0.6068115 at 110iterations 1.9568291E-02 0.3929195 at 120iterations 1.1150014E-02 0.1992035 at 130iterations 6.3423095E-03 0.1315727 at 140iterations 3.6053930E-03 7.2146416E-02 at 150iterations 2.0523577E-03 3.7355185E-02 at 160iterations 1.1698400E-03 2.0317078E-02 at 170iterations 6.6608004E-04 1.4722824E-02 at 180iterations finished qdiffx linear iterations at : 11:26:57 total time elapsed so far: 16.13000 # loops : 180 mean,max change (kT/e) : 6.6608004E-04 1.4722824E-02 energy calculations done at 16.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.27000 DelPhi exited at 11:26:57 16.268u 0.312s 0:16.91 97.9% 0+0k 0+0io 0pf+0w