Wed Feb 15 08:55:46 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:46 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 = 5402 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: 0.4877781 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): -45.68100 22.26100 ymin,ymax (A): -30.60900 42.37500 zmin,zma (A): 10.14500 72.30600 x,y,z range (A): 67.94200 72.98400 62.16100 scale (grids/A): 0.4877781 object centre (A): -11.71000 5.882999 41.22550 number of atom coordinates read : 5402 total number of charged atoms : 5247 net assigned charge : 12.00002 assigned positive charge : 853.1913 centred at (gu) : 89.32305 90.44461 88.24685 assigned negative charge : -841.2001 centred at (gu) : 89.29803 90.49448 88.22227 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8099 nv = 96 ne = 84 npr = 106426 no. pairs analyzed = 106426 no. exposed pairs = 6581 no. arc points = 44461 no. surface atoms = 2219 nbur = 3183 mkacc time = 0.1800000 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 = 1.736000 m= 256 mr = 4305 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4309 ## 681 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 10892 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1193411E-11 5.3885504E-11 midg,1,midg; midg,igrid,midg 1.0071523E-10 4.6765898E-12 1,midg,midg; igrid,midg,midg 3.8054296E-11 7.2244405E-11 gauss-seidel spectral radius is 0.9785556 estimated iterations to convergence 57 setup time was (sec) 0.5400000 now iterating at: 08:55:47 rms-change max change #iterations 5.6759469E-02 9.472683 at 10iterations 3.2563158E-03 0.5512924 at 20iterations 7.9956074E-04 0.1281548 at 30iterations 3.9100816E-04 6.3258171E-02 at 40iterations 1.9531112E-04 3.1832695E-02 at 50iterations finished qdiffx linear iterations at : 08:55:50 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 1.9531112E-04 3.1832695E-02 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 08:55:50 3.604u 0.187s 0:04.27 88.5% 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 Wed Feb 15 2012 at 08:55:50 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 = 5402 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.463334 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): -45.68100 22.26100 ymin,ymax (A): -30.60900 42.37500 zmin,zma (A): 10.14500 72.30600 x,y,z range (A): 67.94200 72.98400 62.16100 scale (grids/A): 1.463334 object centre (A): -11.71000 5.882999 41.22550 number of atom coordinates read : 5402 total number of charged atoms : 5247 net assigned charge : 12.00002 assigned positive charge : 853.1913 centred at (gu) : 87.96747 91.33187 84.73854 assigned negative charge : -841.2001 centred at (gu) : 87.89391 91.48364 84.66673 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 93358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44461 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 26173 mr = 65850 m= 1931 mr = 17437 m= 33 mr = 735 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1983 time to turn everything in is 0.4600000 number of dielectric boundary points 37473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 709 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 38804 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) : 0.4877781 object centre at (A) : -11.71000 5.882999 41.22550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0939550E-04 3.3937788E-03 midg,1,midg; midg,igrid,midg 8.6195217E-03 -2.4664991E-02 1,midg,midg; igrid,midg,midg 1.0574656E-03 1.5007582E-02 gauss-seidel spectral radius is 0.9979518 estimated iterations to convergence 176 setup time was (sec) 0.6700000 now iterating at: 08:55:51 rms-change max change #iterations 3.734459 142.7072 at 10iterations 1.476078 48.70251 at 20iterations 0.5845425 19.52501 at 30iterations 0.2317045 7.909597 at 40iterations 9.1673858E-02 2.713276 at 50iterations 3.6364600E-02 1.188629 at 60iterations 1.4534103E-02 0.5146561 at 70iterations 5.9291576E-03 0.2135506 at 80iterations 2.5602323E-03 8.8293076E-02 at 90iterations 1.2939449E-03 5.0627410E-02 at 100iterations 8.1548531E-04 2.8632164E-02 at 110iterations 5.8791437E-04 2.0945549E-02 at 120iterations finished qdiffx linear iterations at : 08:55:58 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 5.8791437E-04 2.0945549E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 08:55:59 7.965u 0.204s 0:08.68 94.0% 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 Wed Feb 15 2012 at 08:55:59 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 = 5402 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: 2.195002 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): -45.68100 22.26100 ymin,ymax (A): -30.60900 42.37500 zmin,zma (A): 10.14500 72.30600 x,y,z range (A): 67.94200 72.98400 62.16100 scale (grids/A): 2.195002 object centre (A): -11.71000 5.882999 41.22550 number of atom coordinates read : 5402 total number of charged atoms : 5247 net assigned charge : 12.00002 assigned positive charge : 853.1913 centred at (gu) : 86.95088 91.99732 82.10742 assigned negative charge : -841.2001 centred at (gu) : 86.84084 92.22561 82.00021 start vw surface at 0.1400000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 218314 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44461 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 96673 mr = 161850 m= 22339 mr = 76119 m= 2522 mr = 15891 m= 98 mr = 1457 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 6613 time to turn everything in is 1.100000 number of dielectric boundary points 84610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 41765 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) : 1.463334 object centre at (A) : -11.71000 5.882999 41.22550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7710502E-02 5.3483289E-02 midg,1,midg; midg,igrid,midg 0.1662722 -0.8138325 1,midg,midg; igrid,midg,midg -2.6653113E-02 0.2652638 gauss-seidel spectral radius is 0.9991164 estimated iterations to convergence 266 setup time was (sec) 1.330000 now iterating at: 08:56:01 rms-change max change #iterations 10.34354 315.5233 at 10iterations 5.795457 161.6426 at 20iterations 3.229017 69.49727 at 30iterations 1.791379 36.53311 at 40iterations 0.9890302 20.32302 at 50iterations 0.5455168 10.47618 at 60iterations 0.2997519 6.166134 at 70iterations 0.1645519 3.046009 at 80iterations 9.0239599E-02 1.715819 at 90iterations 4.9443789E-02 0.9656143 at 100iterations 2.7102971E-02 0.5040932 at 110iterations 1.4847423E-02 0.3031797 at 120iterations 8.1274286E-03 0.1476440 at 130iterations 4.4718320E-03 8.7186307E-02 at 140iterations 2.4638907E-03 5.3786278E-02 at 150iterations 1.3854058E-03 2.6557922E-02 at 160iterations 8.0181076E-04 1.6160965E-02 at 170iterations 4.9222412E-04 1.1762619E-02 at 180iterations finished qdiffx linear iterations at : 08:56:12 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 4.9222412E-04 1.1762619E-02 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.02000 DelPhi exited at 08:56:13 13.026u 0.219s 0:13.53 97.7% 0+0k 0+0io 0pf+0w