Mon Oct 10 19:35:01 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 Mon Oct 10 2011 at 19:35:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2399 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: 0.6998231 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): -18.39100 31.07600 ymin,ymax (A): -6.560000 40.04700 zmin,zma (A): 35.63300 86.50300 x,y,z range (A): 49.46700 46.60700 50.87000 scale (grids/A): 0.6998231 object centre (A): 6.342501 16.74350 61.06800 number of atom coordinates read : 2399 total number of charged atoms : 2262 net assigned charge : 1.000008 assigned positive charge : 356.9458 centred at (gu) : 90.38587 91.54580 88.71391 assigned negative charge : -355.9465 centred at (gu) : 90.57806 91.55907 88.72725 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8252 nv = 96 ne = 84 npr = 47972 no. pairs analyzed = 47972 no. exposed pairs = 3224 no. arc points = 22196 no. surface atoms = 1069 nbur = 1330 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 600 mr = 4527 m= 6 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2900000 number of dielectric boundary points 4218 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2018 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9015 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7803449E-08 1.0021806E-09 midg,1,midg; midg,igrid,midg 1.0211444E-08 1.5030960E-09 1,midg,midg; igrid,midg,midg 8.9497469E-08 -9.2137192E-08 gauss-seidel spectral radius is 0.9894016 estimated iterations to convergence 79 setup time was (sec) 0.5200000 now iterating at: 19:35:01 rms-change max change #iterations 0.2052065 28.58119 at 10iterations 2.4631189E-02 3.150040 at 20iterations 3.0848715E-03 0.4407835 at 30iterations 4.7118287E-04 7.2273254E-02 at 40iterations 1.1896898E-04 1.8067360E-02 at 50iterations finished qdiffx linear iterations at : 19:35:04 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 1.1896898E-04 1.8067360E-02 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 19:35:05 3.253u 0.174s 0:03.94 86.8% 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 19:35:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2399 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.099469 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): -18.39100 31.07600 ymin,ymax (A): -6.560000 40.04700 zmin,zma (A): 35.63300 86.50300 x,y,z range (A): 49.46700 46.60700 50.87000 scale (grids/A): 2.099469 object centre (A): 6.342501 16.74350 61.06800 number of atom coordinates read : 2399 total number of charged atoms : 2262 net assigned charge : 1.000008 assigned positive charge : 356.9458 centred at (gu) : 91.15693 94.63704 86.14105 assigned negative charge : -355.9465 centred at (gu) : 91.73392 94.67692 86.18160 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 87198 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22196 grid for indexing accessible points = 1.400000 m= 36040 mr = 60407 m= 7722 mr = 27192 m= 680 mr = 5091 m= 21 mr = 262 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 132 time to turn everything in is 0.6300000 number of dielectric boundary points 38708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 84 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 17986 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) : 0.6998231 object centre at (A) : 6.342501 16.74350 61.06800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2267416E-02 7.9655973E-04 midg,1,midg; midg,igrid,midg 1.5075508E-03 -4.4833724E-03 1,midg,midg; igrid,midg,midg 3.9627884E-02 -2.7428182E-02 gauss-seidel spectral radius is 0.9988496 estimated iterations to convergence 233 setup time was (sec) 0.9300000 now iterating at: 19:35:06 rms-change max change #iterations 4.880026 187.3492 at 10iterations 2.422272 81.30985 at 20iterations 1.207274 36.94920 at 30iterations 0.6028984 17.51064 at 40iterations 0.3013572 9.080189 at 50iterations 0.1495275 4.594315 at 60iterations 7.4731573E-02 2.217979 at 70iterations 3.7226003E-02 1.045338 at 80iterations 1.8626362E-02 0.5532541 at 90iterations 9.3223229E-03 0.2706909 at 100iterations 4.6886671E-03 0.1280003 at 110iterations 2.3783473E-03 6.8012238E-02 at 120iterations finished qdiffx linear iterations at : 19:35:12 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 2.3783473E-03 6.8012238E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 19:35:13 7.573u 0.195s 0:08.05 96.3% 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 19:35:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2399 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: 3.149204 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): -18.39100 31.07600 ymin,ymax (A): -6.560000 40.04700 zmin,zma (A): 35.63300 86.50300 x,y,z range (A): 49.46700 46.60700 50.87000 scale (grids/A): 3.149204 object centre (A): 6.342501 16.74350 61.06800 number of atom coordinates read : 2399 total number of charged atoms : 2262 net assigned charge : 1.000008 assigned positive charge : 356.9458 centred at (gu) : 91.73522 96.95536 84.21152 assigned negative charge : -355.9465 centred at (gu) : 92.60075 97.01534 84.27228 start vw surface at 0.1400000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 200788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22196 grid for indexing accessible points = 1.400000 m= 109493 mr = 145973 m= 47878 mr = 90282 m= 14727 mr = 39085 m= 2875 mr = 11366 m= 276 mr = 1941 m= 13 mr = 143 m= 0 mr = 1 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 437 time to turn everything in is 2.010000 number of dielectric boundary points 87259 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 18096 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) : 2.099469 object centre at (A) : 6.342501 16.74350 61.06800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4323519 0.1985344 midg,1,midg; midg,igrid,midg -0.1064626 -8.8854708E-02 1,midg,midg; igrid,midg,midg 0.3441274 -0.2380768 gauss-seidel spectral radius is 0.9993124 estimated iterations to convergence 301 setup time was (sec) 2.310000 now iterating at: 19:35:15 rms-change max change #iterations 11.03618 418.5327 at 10iterations 6.578619 133.8107 at 20iterations 3.930291 76.42668 at 30iterations 2.328757 38.14492 at 40iterations 1.381163 24.56054 at 50iterations 0.8157553 17.30168 at 60iterations 0.4807801 8.606152 at 70iterations 0.2832061 4.677464 at 80iterations 0.1665672 2.821701 at 90iterations 9.8128408E-02 1.550854 at 100iterations 5.7634726E-02 0.9580970 at 110iterations 3.3876617E-02 0.5391593 at 120iterations 1.9887287E-02 0.3400841 at 130iterations 1.1684299E-02 0.1953926 at 140iterations 6.8535111E-03 0.1038813 at 150iterations 4.0307180E-03 6.6851139E-02 at 160iterations 2.3690548E-03 3.8542747E-02 at 170iterations 1.3971240E-03 2.2403717E-02 at 180iterations finished qdiffx linear iterations at : 19:35:26 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 1.3971240E-03 2.2403717E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 19:35:26 12.963u 0.224s 0:13.60 96.9% 0+0k 0+0io 0pf+0w