Tue Oct 11 03:20:12 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 03:20:12 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1872 !!! WARNING: no radius record for F1 F1 5 !!! WARNING: no radius record for F2 F2 6 !!! WARNING: no radius record for F1 F1 7 !!! WARNING: no radius record for F2 F2 8 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7139562 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): 18.94100 64.50700 ymin,ymax (A): -10.96300 34.98800 zmin,zma (A): 0.8830000 50.74600 x,y,z range (A): 45.56599 45.95100 49.86300 scale (grids/A): 0.7139562 object centre (A): 41.72400 12.01250 25.81450 number of atom coordinates read : 1872 total number of charged atoms : 1701 net assigned charge : 6.000002 assigned positive charge : 277.9151 centred at (gu) : 90.71013 90.03628 90.05390 assigned negative charge : -271.9153 centred at (gu) : 90.79448 90.41944 90.14121 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6493 nv = 96 ne = 84 npr = 36531 no. pairs analyzed = 36531 no. exposed pairs = 2470 no. arc points = 17655 no. surface atoms = 830 nbur = 1042 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 3421 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.2700000 number of dielectric boundary points 3444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1537 ## 127 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6920 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0186387E-07 1.6164426E-08 midg,1,midg; midg,igrid,midg 2.4173255E-07 -1.3925980E-07 1,midg,midg; igrid,midg,midg 8.8638572E-08 1.9609121E-08 gauss-seidel spectral radius is 0.9897590 estimated iterations to convergence 80 setup time was (sec) 0.5000000 now iterating at: 03:20:13 rms-change max change #iterations 0.1901665 29.15427 at 10iterations 2.3887357E-02 3.461697 at 20iterations 2.9396694E-03 0.4294291 at 30iterations 3.6358100E-04 5.6167603E-02 at 40iterations 4.5791738E-05 6.6261292E-03 at 50iterations finished qdiffx linear iterations at : 03:20:15 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 4.5791738E-05 6.6261292E-03 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 03:20:16 3.263u 0.189s 0:03.91 87.9% 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 03:20:16 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1872 !!! WARNING: no radius record for F1 F1 5 !!! WARNING: no radius record for F2 F2 6 !!! WARNING: no radius record for F1 F1 7 !!! WARNING: no radius record for F2 F2 8 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.141869 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): 18.94100 64.50700 ymin,ymax (A): -10.96300 34.98800 zmin,zma (A): 0.8830000 50.74600 x,y,z range (A): 45.56599 45.95100 49.86300 scale (grids/A): 2.141869 object centre (A): 41.72400 12.01250 25.81450 number of atom coordinates read : 1872 total number of charged atoms : 1701 net assigned charge : 6.000002 assigned positive charge : 277.9151 centred at (gu) : 92.13030 90.10873 90.16178 assigned negative charge : -271.9153 centred at (gu) : 92.38383 91.25858 90.42397 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68274 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17655 grid for indexing accessible points = 1.400000 m= 26194 mr = 45650 m= 4957 mr = 19263 m= 447 mr = 3091 m= 15 mr = 191 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 927 time to turn everything in is 0.5200000 number of dielectric boundary points 31692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 13518 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) : 0.7139562 object centre at (A) : 41.72400 12.01250 25.81450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6988351E-02 -2.2770022E-03 midg,1,midg; midg,igrid,midg 7.5377069E-02 -8.8579744E-02 1,midg,midg; igrid,midg,midg 2.2763850E-02 4.5916069E-02 gauss-seidel spectral radius is 0.9988361 estimated iterations to convergence 232 setup time was (sec) 0.8100000 now iterating at: 03:20:17 rms-change max change #iterations 4.368752 233.3291 at 10iterations 2.157932 71.98022 at 20iterations 1.065507 36.14574 at 30iterations 0.5270408 17.63541 at 40iterations 0.2616403 8.421078 at 50iterations 0.1295812 3.893206 at 60iterations 6.4291500E-02 2.010204 at 70iterations 3.1740755E-02 1.044372 at 80iterations 1.5781133E-02 0.4875112 at 90iterations 7.8379484E-03 0.2670212 at 100iterations 3.8722090E-03 0.1170912 at 110iterations 1.9233733E-03 6.2230349E-02 at 120iterations finished qdiffx linear iterations at : 03:20:23 total time elapsed so far: 7.180000 # loops : 120 mean,max change (kT/e) : 1.9233733E-03 6.2230349E-02 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.360000 DelPhi exited at 03:20:24 7.359u 0.212s 0:07.87 96.0% 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 03:20:24 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1872 !!! WARNING: no radius record for F1 F1 5 !!! WARNING: no radius record for F2 F2 6 !!! WARNING: no radius record for F1 F1 7 !!! WARNING: no radius record for F2 F2 8 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.212803 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): 18.94100 64.50700 ymin,ymax (A): -10.96300 34.98800 zmin,zma (A): 0.8830000 50.74600 x,y,z range (A): 45.56599 45.95100 49.86300 scale (grids/A): 3.212803 object centre (A): 41.72400 12.01250 25.81450 number of atom coordinates read : 1872 total number of charged atoms : 1701 net assigned charge : 6.000002 assigned positive charge : 277.9151 centred at (gu) : 93.19540 90.16321 90.24268 assigned negative charge : -271.9153 centred at (gu) : 93.57585 91.88805 90.63613 start vw surface at 0.1400000 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 157347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17655 grid for indexing accessible points = 1.400000 m= 81109 mr = 110518 m= 32607 mr = 66015 m= 9014 mr = 26094 m= 1709 mr = 6690 m= 175 mr = 1156 m= 9 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.7500001 no. cavity mid-points inaccessible to solvent = 3124 time to turn everything in is 1.590000 number of dielectric boundary points 71413 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 13608 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) : 2.141869 object centre at (A) : 41.72400 12.01250 25.81450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2813291 -7.9225458E-02 midg,1,midg; midg,igrid,midg 0.5075987 -1.020381 1,midg,midg; igrid,midg,midg 0.1119947 0.4950961 gauss-seidel spectral radius is 0.9993107 estimated iterations to convergence 300 setup time was (sec) 1.890000 now iterating at: 03:20:26 rms-change max change #iterations 9.923923 308.7429 at 10iterations 5.891985 148.1376 at 20iterations 3.500024 100.8390 at 30iterations 2.059658 40.58389 at 40iterations 1.215433 25.90353 at 50iterations 0.7151984 12.80322 at 60iterations 0.4203101 8.513657 at 70iterations 0.2471705 4.494305 at 80iterations 0.1450155 2.677085 at 90iterations 8.4973536E-02 1.520870 at 100iterations 4.9761061E-02 0.8847580 at 110iterations 2.9232508E-02 0.6240082 at 120iterations 1.7087540E-02 0.3665916 at 130iterations 1.0024101E-02 0.1700408 at 140iterations 5.8735800E-03 0.1045592 at 150iterations 3.4317817E-03 6.1944485E-02 at 160iterations 2.0121711E-03 4.2565346E-02 at 170iterations 1.1775509E-03 2.0339966E-02 at 180iterations finished qdiffx linear iterations at : 03:20:36 total time elapsed so far: 12.00000 # loops : 180 mean,max change (kT/e) : 1.1775509E-03 2.0339966E-02 energy calculations done at 12.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.17000 DelPhi exited at 03:20:37 12.176u 0.211s 0:12.71 97.4% 0+0k 0+0io 0pf+0w