Mon Oct 10 17:05:28 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 Mon Oct 10 2011 at 17:05:28 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4660 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 808 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5238761 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): -25.01700 39.56400 ymin,ymax (A): -18.08500 45.99400 zmin,zma (A): 7.121000 75.07600 x,y,z range (A): 64.58100 64.07900 67.95500 scale (grids/A): 0.5238761 object centre (A): 7.273501 13.95450 41.09850 number of atom coordinates read : 4660 total number of charged atoms : 4416 net assigned charge : 6.706034 assigned positive charge : 704.1336 centred at (gu) : 91.53271 88.83526 87.75198 assigned negative charge : -697.4316 centred at (gu) : 91.64388 88.94017 87.62560 start vw surface at 0.1900000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8240 nv = 96 ne = 84 npr = 93087 no. pairs analyzed = 93087 no. exposed pairs = 6161 no. arc points = 42293 no. surface atoms = 2065 nbur = 2595 mkacc time = 0.2700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 312 mr = 4193 m= 0 mr = 13 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4090 ## 544 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 10752 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8731149E-10 4.0890050E-10 midg,1,midg; midg,igrid,midg 8.5943824E-10 -2.0358690E-10 1,midg,midg; igrid,midg,midg 4.4679663E-10 -4.6300699E-10 gauss-seidel spectral radius is 0.9813581 estimated iterations to convergence 60 setup time was (sec) 0.7700000 now iterating at: 17:05:29 rms-change max change #iterations 7.5590059E-02 10.60321 at 10iterations 4.8748651E-03 0.8107338 at 20iterations 7.1866199E-04 9.3574524E-02 at 30iterations 2.6808525E-04 4.0084600E-02 at 40iterations 1.1053401E-04 1.7810702E-02 at 50iterations finished qdiffx linear iterations at : 17:05:31 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 1.1053401E-04 1.7810702E-02 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 17:05:32 3.737u 0.186s 0:04.27 91.5% 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 Mon Oct 10 2011 at 17:05:32 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4660 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 808 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.571628 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): -25.01700 39.56400 ymin,ymax (A): -18.08500 45.99400 zmin,zma (A): 7.121000 75.07600 x,y,z range (A): 64.58100 64.07900 67.95500 scale (grids/A): 1.571628 object centre (A): 7.273501 13.95450 41.09850 number of atom coordinates read : 4660 total number of charged atoms : 4416 net assigned charge : 6.706034 assigned positive charge : 704.1336 centred at (gu) : 94.59679 86.50455 83.25427 assigned negative charge : -697.4316 centred at (gu) : 94.93102 86.82025 82.87640 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 92411 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42293 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 27129 mr = 62776 m= 2525 mr = 17829 m= 55 mr = 1051 m= 0 mr = 6 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 40458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 454 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 33438 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) : 0.5238761 object centre at (A) : 7.273501 13.95450 41.09850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9540269E-03 2.1150881E-02 midg,1,midg; midg,igrid,midg 7.5510582E-03 -1.1218812E-02 1,midg,midg; igrid,midg,midg 1.2560025E-02 4.7432556E-04 gauss-seidel spectral radius is 0.9982080 estimated iterations to convergence 188 setup time was (sec) 1.000000 now iterating at: 17:05:33 rms-change max change #iterations 3.992230 176.9267 at 10iterations 1.672208 69.06799 at 20iterations 0.7011011 23.32407 at 30iterations 0.2948592 9.595432 at 40iterations 0.1234987 3.590302 at 50iterations 5.2005507E-02 1.684689 at 60iterations 2.1866163E-02 0.7280836 at 70iterations 9.2273820E-03 0.2765160 at 80iterations 3.8920771E-03 0.1240005 at 90iterations 1.6716414E-03 5.7542324E-02 at 100iterations 7.3888793E-04 2.1347046E-02 at 110iterations 3.5287169E-04 1.1738777E-02 at 120iterations finished qdiffx linear iterations at : 17:05:40 total time elapsed so far: 8.130000 # loops : 120 mean,max change (kT/e) : 3.5287169E-04 1.1738777E-02 energy calculations done at 8.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.340000 DelPhi exited at 17:05:41 8.339u 0.260s 0:08.91 96.4% 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 Mon Oct 10 2011 at 17:05:41 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4660 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 808 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.357442 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): -25.01700 39.56400 ymin,ymax (A): -18.08500 45.99400 zmin,zma (A): 7.121000 75.07600 x,y,z range (A): 64.58100 64.07900 67.95500 scale (grids/A): 2.357442 object centre (A): 7.273501 13.95450 41.09850 number of atom coordinates read : 4660 total number of charged atoms : 4416 net assigned charge : 6.706034 assigned positive charge : 704.1336 centred at (gu) : 96.89492 84.75630 79.88107 assigned negative charge : -697.4316 centred at (gu) : 97.39644 85.23026 79.31444 start vw surface at 0.2200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 215368 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42293 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 96654 mr = 154526 m= 24835 mr = 74879 m= 3636 mr = 17609 m= 219 mr = 2216 m= 5 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.670000 number of dielectric boundary points 91388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 35253 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) : 1.571628 object centre at (A) : 7.273501 13.95450 41.09850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5925935 0.4569141 midg,1,midg; midg,igrid,midg 8.3116680E-02 -0.2342957 1,midg,midg; igrid,midg,midg 0.1865946 2.4303565E-02 gauss-seidel spectral radius is 0.9991875 estimated iterations to convergence 277 setup time was (sec) 2.020000 now iterating at: 17:05:43 rms-change max change #iterations 10.59057 576.4162 at 10iterations 6.123939 217.9717 at 20iterations 3.510087 68.98669 at 30iterations 2.001101 47.66002 at 40iterations 1.135234 26.53915 at 50iterations 0.6442979 12.75754 at 60iterations 0.3645243 7.182577 at 70iterations 0.2054366 4.262032 at 80iterations 0.1156424 2.350739 at 90iterations 6.4990744E-02 1.316499 at 100iterations 3.6559019E-02 0.6464605 at 110iterations 2.0548988E-02 0.4358025 at 120iterations 1.1513998E-02 0.2149363 at 130iterations 6.4614350E-03 0.1160812 at 140iterations 3.6249878E-03 6.5360546E-02 at 150iterations 2.0334073E-03 3.7017822E-02 at 160iterations 1.1392760E-03 2.0237923E-02 at 170iterations 6.3964736E-04 1.2071609E-02 at 180iterations finished qdiffx linear iterations at : 17:05:55 total time elapsed so far: 13.33000 # loops : 180 mean,max change (kT/e) : 6.3964736E-04 1.2071609E-02 energy calculations done at 13.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 17:05:55 13.546u 0.203s 0:14.23 96.5% 0+0k 0+0io 0pf+0w