Sat Jan 28 03:07:25 PST 2012 #!/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 Jan 28 2012 at 03:07:25 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 ! Automatically converted by prot2crg.py # of charge parameter records: 960 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1727 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 !!! WARNING: ZN4 490 has a net charge of 1.6000 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: 0.7381297 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): -51.99600 -3.766000 ymin,ymax (A): 3.052000 47.84600 zmin,zma (A): 42.25300 87.01000 x,y,z range (A): 48.23000 44.79400 44.75700 scale (grids/A): 0.7381297 object centre (A): -27.88100 25.44900 64.63150 number of atom coordinates read : 1727 total number of charged atoms : 1587 net assigned charge : -6.999991 assigned positive charge : 262.0143 centred at (gu) : 89.33454 90.98610 89.55514 assigned negative charge : -269.0143 centred at (gu) : 89.47717 90.96235 89.97975 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6581 nv = 96 ne = 84 npr = 34965 no. pairs analyzed = 34965 no. exposed pairs = 2316 no. arc points = 16428 no. surface atoms = 788 nbur = 939 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 3579 m= 4 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.1800000 number of dielectric boundary points 3390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1311 ## 96 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3449302E-07 -4.4454316E-07 midg,1,midg; midg,igrid,midg -1.1689917E-07 -1.2028117E-07 1,midg,midg; igrid,midg,midg -4.2752482E-09 -2.1118086E-07 gauss-seidel spectral radius is 0.9904004 estimated iterations to convergence 83 setup time was (sec) 0.3800000 now iterating at: 03:07:26 rms-change max change #iterations 0.2282209 40.46281 at 10iterations 3.0240027E-02 4.219751 at 20iterations 3.9569419E-03 0.5325165 at 30iterations 5.3271960E-04 6.9335938E-02 at 40iterations 7.0184171E-05 9.5720291E-03 at 50iterations finished qdiffx linear iterations at : 03:07:29 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 7.0184171E-05 9.5720291E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 03:07:29 3.463u 0.195s 0:03.97 91.9% 0+0k 1896+45504io 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 Sat Jan 28 2012 at 03:07:29 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 ! Automatically converted by prot2crg.py # of charge parameter records: 960 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1727 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 !!! WARNING: ZN4 490 has a net charge of 1.6000 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: 2.214389 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): -51.99600 -3.766000 ymin,ymax (A): 3.052000 47.84600 zmin,zma (A): 42.25300 87.01000 x,y,z range (A): 48.23000 44.79400 44.75700 scale (grids/A): 2.214389 object centre (A): -27.88100 25.44900 64.63150 number of atom coordinates read : 1727 total number of charged atoms : 1587 net assigned charge : -6.999991 assigned positive charge : 262.0143 centred at (gu) : 88.00394 92.95842 88.66547 assigned negative charge : -269.0143 centred at (gu) : 88.43172 92.88731 89.93965 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 68460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16428 grid for indexing accessible points = 1.400000 m= 27669 mr = 46186 m= 5961 mr = 20912 m= 607 mr = 4086 m= 18 mr = 304 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 465 time to turn everything in is 0.4600000 number of dielectric boundary points 31225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 12631 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) : 0.7381297 object centre at (A) : -27.88100 25.44900 64.63150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2554634E-02 -0.1198870 midg,1,midg; midg,igrid,midg -6.8506569E-02 -7.4634828E-02 1,midg,midg; igrid,midg,midg 5.1300313E-02 -7.1459964E-02 gauss-seidel spectral radius is 0.9988878 estimated iterations to convergence 237 setup time was (sec) 0.6600000 now iterating at: 03:07:30 rms-change max change #iterations 4.696461 194.9607 at 10iterations 2.366255 90.70482 at 20iterations 1.191630 41.44434 at 30iterations 0.5997567 20.62580 at 40iterations 0.3027911 9.770597 at 50iterations 0.1528365 4.469189 at 60iterations 7.7272013E-02 2.426789 at 70iterations 3.8936019E-02 1.236370 at 80iterations 1.9626597E-02 0.5877514 at 90iterations 9.9113928E-03 0.3029861 at 100iterations 4.9956767E-03 0.1584969 at 110iterations 2.5208243E-03 8.0226898E-02 at 120iterations finished qdiffx linear iterations at : 03:07:37 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.5208243E-03 8.0226898E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 03:07:38 7.989u 0.241s 0:08.51 96.5% 0+0k 0+45112io 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 Jan 28 2012 at 03:07:38 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 ! Automatically converted by prot2crg.py # of charge parameter records: 960 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1727 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 !!! WARNING: ZN4 490 has a net charge of 1.6000 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: 3.321584 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): -51.99600 -3.766000 ymin,ymax (A): 3.052000 47.84600 zmin,zma (A): 42.25300 87.01000 x,y,z range (A): 48.23000 44.79400 44.75700 scale (grids/A): 3.321584 object centre (A): -27.88100 25.44900 64.63150 number of atom coordinates read : 1727 total number of charged atoms : 1587 net assigned charge : -6.999991 assigned positive charge : 262.0143 centred at (gu) : 87.00599 94.43769 87.99830 assigned negative charge : -269.0143 centred at (gu) : 87.64762 94.33109 89.90958 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 157383 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16428 grid for indexing accessible points = 1.400000 m= 83577 mr = 111218 m= 36585 mr = 68966 m= 11445 mr = 30292 m= 2458 mr = 8969 m= 321 mr = 1822 m= 12 mr = 217 m= 0 mr = 3 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 1699 time to turn everything in is 1.390000 number of dielectric boundary points 70294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 12696 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) : 2.214389 object centre at (A) : -27.88100 25.44900 64.63150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7468711E-02 -1.213358 midg,1,midg; midg,igrid,midg -0.4345159 -0.6080254 1,midg,midg; igrid,midg,midg 0.1339462 -1.194408 gauss-seidel spectral radius is 0.9993070 estimated iterations to convergence 300 setup time was (sec) 1.620000 now iterating at: 03:07:39 rms-change max change #iterations 10.17195 331.7249 at 10iterations 5.983144 130.6263 at 20iterations 3.513725 61.88446 at 30iterations 2.059982 39.74994 at 40iterations 1.205233 22.51516 at 50iterations 0.7071662 12.14644 at 60iterations 0.4132693 7.074145 at 70iterations 0.2421795 4.644207 at 80iterations 0.1416092 2.713116 at 90iterations 8.2672015E-02 1.700973 at 100iterations 4.8482209E-02 0.8595352 at 110iterations 2.8290657E-02 0.4914303 at 120iterations 1.6511135E-02 0.2868347 at 130iterations 9.6741626E-03 0.1716309 at 140iterations 5.6453878E-03 9.7236633E-02 at 150iterations 3.3129044E-03 6.1463475E-02 at 160iterations 1.9343041E-03 3.3401489E-02 at 170iterations 1.1348660E-03 2.2746086E-02 at 180iterations finished qdiffx linear iterations at : 03:07:52 total time elapsed so far: 14.31000 # loops : 180 mean,max change (kT/e) : 1.1348660E-03 2.2746086E-02 energy calculations done at 14.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.45000 DelPhi exited at 03:07:53 14.456u 0.236s 0:14.98 97.9% 0+0k 0+45104io 0pf+0w