Mon Oct 10 14:37:35 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 14:37:35 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2710 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5808357 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): -8.582000 52.70900 ymin,ymax (A): -15.88800 34.23400 zmin,zma (A): 77.59299 130.6640 x,y,z range (A): 61.29100 50.12200 53.07101 scale (grids/A): 0.5808357 object centre (A): 22.06350 9.172998 104.1285 number of atom coordinates read : 2710 total number of charged atoms : 2568 net assigned charge : -2.599991 assigned positive charge : 424.3755 centred at (gu) : 92.19482 89.87520 89.28868 assigned negative charge : -426.9763 centred at (gu) : 92.10181 89.94962 89.37376 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6092 nv = 96 ne = 84 npr = 52855 no. pairs analyzed = 52855 no. exposed pairs = 3820 no. arc points = 26263 no. surface atoms = 1281 nbur = 1429 mkacc time = 8.9999996E-02 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 = 1.484000 m= 283 mr = 2967 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2766 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7764 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3993163E-09 -2.1192317E-09 midg,1,midg; midg,igrid,midg 9.7908848E-10 -2.2034150E-09 1,midg,midg; igrid,midg,midg -1.6080257E-09 2.3069688E-09 gauss-seidel spectral radius is 0.9846834 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 14:37:36 rms-change max change #iterations 9.7683981E-02 16.67326 at 10iterations 7.4649588E-03 1.321400 at 20iterations 6.0366682E-04 9.7148895E-02 at 30iterations 5.5227440E-05 9.6015930E-03 at 40iterations 8.8754914E-06 1.4743805E-03 at 50iterations finished qdiffx linear iterations at : 14:37:39 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 8.8754914E-06 1.4743805E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 14:37:39 3.637u 0.215s 0:04.22 90.9% 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 Mon Oct 10 2011 at 14:37:40 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2710 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 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: 1.742507 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): -8.582000 52.70900 ymin,ymax (A): -15.88800 34.23400 zmin,zma (A): 77.59299 130.6640 x,y,z range (A): 61.29100 50.12200 53.07101 scale (grids/A): 1.742507 object centre (A): 22.06350 9.172998 104.1285 number of atom coordinates read : 2710 total number of charged atoms : 2568 net assigned charge : -2.599991 assigned positive charge : 424.3755 centred at (gu) : 96.58375 89.62501 87.86528 assigned negative charge : -426.9763 centred at (gu) : 96.30507 89.84836 88.12131 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66290 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26263 grid for indexing accessible points = 1.400000 m= 21755 mr = 43711 m= 2804 mr = 14412 m= 112 mr = 1353 m= 0 mr = 24 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 31461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 220 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19885 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) : 0.5808357 object centre at (A) : 22.06350 9.172998 104.1285 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0538566E-03 -2.7411191E-02 midg,1,midg; midg,igrid,midg -4.6017854E-03 -1.5066371E-02 1,midg,midg; igrid,midg,midg 1.7187966E-02 4.1608837E-02 gauss-seidel spectral radius is 0.9983969 estimated iterations to convergence 198 setup time was (sec) 0.5900000 now iterating at: 14:37:40 rms-change max change #iterations 3.787663 173.1516 at 10iterations 1.654426 64.76816 at 20iterations 0.7286197 27.04422 at 30iterations 0.3188800 11.84526 at 40iterations 0.1401265 5.266557 at 50iterations 6.1560567E-02 2.130508 at 60iterations 2.7066413E-02 1.097938 at 70iterations 1.1884360E-02 0.4157562 at 80iterations 5.2455389E-03 0.2018394 at 90iterations 2.3035514E-03 8.4701538E-02 at 100iterations 1.0118718E-03 3.7060261E-02 at 110iterations 4.4519812E-04 1.5632153E-02 at 120iterations finished qdiffx linear iterations at : 14:37:48 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 4.4519812E-04 1.5632153E-02 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 14:37:48 8.235u 0.275s 0:08.81 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 14:37:48 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2710 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 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: 2.613760 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): -8.582000 52.70900 ymin,ymax (A): -15.88800 34.23400 zmin,zma (A): 77.59299 130.6640 x,y,z range (A): 61.29100 50.12200 53.07101 scale (grids/A): 2.613760 object centre (A): 22.06350 9.172998 104.1285 number of atom coordinates read : 2710 total number of charged atoms : 2568 net assigned charge : -2.599991 assigned positive charge : 424.3755 centred at (gu) : 99.87560 89.43737 86.79793 assigned negative charge : -426.9763 centred at (gu) : 99.45757 89.77236 87.18204 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 153312 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26263 grid for indexing accessible points = 1.400000 m= 72357 mr = 106916 m= 22845 mr = 55963 m= 4450 mr = 16624 m= 483 mr = 2867 m= 15 mr = 254 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 70838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 20532 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) : 1.742507 object centre at (A) : 22.06350 9.172998 104.1285 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1438736E-02 -0.3645352 midg,1,midg; midg,igrid,midg -7.3823072E-02 -0.1719685 1,midg,midg; igrid,midg,midg 0.3441541 0.4834612 gauss-seidel spectral radius is 0.9992000 estimated iterations to convergence 279 setup time was (sec) 1.120000 now iterating at: 14:37:50 rms-change max change #iterations 9.508507 284.5513 at 10iterations 5.504159 137.0004 at 20iterations 3.157251 73.39602 at 30iterations 1.800267 39.26234 at 40iterations 1.023216 21.99079 at 50iterations 0.5800445 13.40574 at 60iterations 0.3276441 7.483355 at 70iterations 0.1853525 3.579316 at 80iterations 0.1047583 2.383570 at 90iterations 5.8884539E-02 1.500069 at 100iterations 3.3208907E-02 0.7220893 at 110iterations 1.8724728E-02 0.3923492 at 120iterations 1.0541204E-02 0.1983299 at 130iterations 5.9286086E-03 0.1196518 at 140iterations 3.3299217E-03 6.6938400E-02 at 150iterations 1.8705054E-03 3.8736343E-02 at 160iterations 1.0563581E-03 2.1346092E-02 at 170iterations 5.9441041E-04 1.1704445E-02 at 180iterations finished qdiffx linear iterations at : 14:38:01 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 5.9441041E-04 1.1704445E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 14:38:01 12.417u 0.305s 0:13.10 97.0% 0+0k 0+0io 0pf+0w