Tue Oct 11 05:23:34 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 Tue Oct 11 2011 at 05:23:34 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2234 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6961691 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): 19.84000 63.23300 ymin,ymax (A): -3.477000 33.56600 zmin,zma (A): 20.10700 71.24400 x,y,z range (A): 43.39300 37.04300 51.13700 scale (grids/A): 0.6961691 object centre (A): 41.53650 15.04450 45.67550 number of atom coordinates read : 2234 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 90.17767 89.66336 89.59449 assigned negative charge : -303.7472 centred at (gu) : 90.34990 89.68302 89.56396 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6800 nv = 96 ne = 84 npr = 40576 no. pairs analyzed = 40576 no. exposed pairs = 2522 no. arc points = 17067 no. surface atoms = 867 nbur = 1367 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 444 mr = 3903 m= 5 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3245 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1674 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7614 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0004590E-08 5.5346291E-08 midg,1,midg; midg,igrid,midg 5.9552249E-08 3.8619554E-08 1,midg,midg; igrid,midg,midg 1.0776905E-07 -1.7592685E-08 gauss-seidel spectral radius is 0.9892446 estimated iterations to convergence 79 setup time was (sec) 0.6100000 now iterating at: 05:23:34 rms-change max change #iterations 0.1829004 26.45335 at 10iterations 2.1798210E-02 3.141693 at 20iterations 2.7569914E-03 0.3785629 at 30iterations 4.4106215E-04 5.5853844E-02 at 40iterations 1.0949338E-04 1.5495300E-02 at 50iterations finished qdiffx linear iterations at : 05:23:38 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 1.0949338E-04 1.5495300E-02 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 05:23:38 3.994u 0.159s 0:04.45 93.0% 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 Oct 11 2011 at 05:23:38 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 # of charge parameter records: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2234 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.088507 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): 19.84000 63.23300 ymin,ymax (A): -3.477000 33.56600 zmin,zma (A): 20.10700 71.24400 x,y,z range (A): 43.39300 37.04300 51.13700 scale (grids/A): 2.088507 object centre (A): 41.53650 15.04450 45.67550 number of atom coordinates read : 2234 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 90.53293 88.99028 88.78359 assigned negative charge : -303.7472 centred at (gu) : 91.04980 89.04931 88.69199 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 72000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17067 grid for indexing accessible points = 1.400000 m= 29283 mr = 51164 m= 5723 mr = 22355 m= 503 mr = 3835 m= 13 mr = 253 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 29915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 15308 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) : 0.6961691 object centre at (A) : 41.53650 15.04450 45.67550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6322543E-02 4.3250885E-02 midg,1,midg; midg,igrid,midg 2.5316084E-02 1.1873168E-02 1,midg,midg; igrid,midg,midg 4.0000115E-02 1.1839081E-02 gauss-seidel spectral radius is 0.9987955 estimated iterations to convergence 228 setup time was (sec) 1.070000 now iterating at: 05:23:40 rms-change max change #iterations 4.414152 202.8004 at 10iterations 2.171352 82.30576 at 20iterations 1.060826 32.41339 at 30iterations 0.5238307 18.45045 at 40iterations 0.2574752 8.901284 at 50iterations 0.1265749 4.134917 at 60iterations 6.2210836E-02 1.998691 at 70iterations 3.0612223E-02 0.9488025 at 80iterations 1.5143665E-02 0.4544992 at 90iterations 7.5308615E-03 0.2149963 at 100iterations 3.7586531E-03 0.1244650 at 110iterations 1.9208629E-03 6.3320160E-02 at 120iterations finished qdiffx linear iterations at : 05:23:48 total time elapsed so far: 9.460000 # loops : 120 mean,max change (kT/e) : 1.9208629E-03 6.3320160E-02 energy calculations done at 9.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.690000 DelPhi exited at 05:23:49 9.693u 0.276s 0:10.60 93.9% 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 Tue Oct 11 2011 at 05:23:49 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2234 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.132761 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): 19.84000 63.23300 ymin,ymax (A): -3.477000 33.56600 zmin,zma (A): 20.10700 71.24400 x,y,z range (A): 43.39300 37.04300 51.13700 scale (grids/A): 3.132761 object centre (A): 41.53650 15.04450 45.67550 number of atom coordinates read : 2234 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 90.79924 88.48544 88.17537 assigned negative charge : -303.7472 centred at (gu) : 91.57471 88.57404 88.03806 start vw surface at 0.1900000 fill in re-entrant regions at 0.9800000 boundary points on vw surface= 165869 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17067 grid for indexing accessible points = 1.400000 m= 91027 mr = 123035 m= 37360 mr = 75933 m= 10717 mr = 30744 m= 2076 mr = 8393 m= 209 mr = 1549 m= 3 mr = 123 m= 0 mr = 2 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.230000 number of dielectric boundary points 67482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.410000 number of grid points assigned charge 15432 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) : 2.088507 object centre at (A) : 41.53650 15.04450 45.67550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3569866 0.2966539 midg,1,midg; midg,igrid,midg 0.2077771 0.1045738 1,midg,midg; igrid,midg,midg 0.3253036 0.2621697 gauss-seidel spectral radius is 0.9992859 estimated iterations to convergence 295 setup time was (sec) 2.630000 now iterating at: 05:23:52 rms-change max change #iterations 9.920670 382.2950 at 10iterations 5.874637 138.0323 at 20iterations 3.465420 84.67629 at 30iterations 2.038801 39.46627 at 40iterations 1.197205 26.02283 at 50iterations 0.7023336 13.44753 at 60iterations 0.4095805 8.719812 at 70iterations 0.2404731 4.405123 at 80iterations 0.1404228 2.936991 at 90iterations 8.2014926E-02 1.528455 at 100iterations 4.8029564E-02 0.9775381 at 110iterations 2.8104834E-02 0.5013614 at 120iterations 1.6555222E-02 0.3412828 at 130iterations 9.8882960E-03 0.1660647 at 140iterations 5.9981351E-03 0.1078949 at 150iterations 3.7383770E-03 6.7209244E-02 at 160iterations 2.4531311E-03 4.6600342E-02 at 170iterations 1.7050719E-03 3.1738281E-02 at 180iterations finished qdiffx linear iterations at : 05:24:05 total time elapsed so far: 15.90000 # loops : 180 mean,max change (kT/e) : 1.7050719E-03 3.1738281E-02 energy calculations done at 15.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.14000 DelPhi exited at 05:24:06 16.142u 0.268s 0:16.69 98.2% 0+0k 0+0io 0pf+0w