Tue Jan 24 16:49:35 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.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 Jan 24 2012 at 16:49:35 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3778 !!! WARNING: CA1 191 has a net charge of 2.0000 !!! WARNING: CA2 192 has a net charge of 2.0000 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: 0.5502574 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): -75.06100 -13.25200 ymin,ymax (A): 39.09400 98.36600 zmin,zma (A): 7.633000 72.33000 x,y,z range (A): 61.80900 59.27201 64.69700 scale (grids/A): 0.5502574 object centre (A): -44.15650 68.73000 39.98150 number of atom coordinates read : 3778 total number of charged atoms : 3648 net assigned charge : 46.00005 assigned positive charge : 596.6970 centred at (gu) : 90.88634 89.15891 88.07118 assigned negative charge : -550.7004 centred at (gu) : 90.77749 89.28797 88.15697 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7616 nv = 96 ne = 84 npr = 65413 no. pairs analyzed = 65413 no. exposed pairs = 6040 no. arc points = 45815 no. surface atoms = 1985 nbur = 1793 mkacc time = 0.1400000 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 = 1.568000 m= 301 mr = 2885 m= 0 mr = 5 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 5027 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4599 ## 678 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 9847 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6151609E-09 1.5933835E-09 midg,1,midg; midg,igrid,midg 5.5695635E-09 1.7015019E-09 1,midg,midg; igrid,midg,midg 1.8441644E-09 5.3962097E-09 gauss-seidel spectral radius is 0.9830655 estimated iterations to convergence 63 setup time was (sec) 0.5000000 now iterating at: 16:49:36 rms-change max change #iterations 8.7981448E-02 13.60556 at 10iterations 6.5038544E-03 0.9973412 at 20iterations 9.1806962E-04 9.7789764E-02 at 30iterations 2.3422133E-04 1.6530991E-02 at 40iterations 6.5737484E-05 4.6520233E-03 at 50iterations finished qdiffx linear iterations at : 16:49:39 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 6.5737484E-05 4.6520233E-03 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 16:49:39 3.584u 0.175s 0:04.21 89.0% 0+0k 0+46528io 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 Jan 24 2012 at 16:49:39 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3778 !!! WARNING: CA1 191 has a net charge of 2.0000 !!! WARNING: CA2 192 has a net charge of 2.0000 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: 1.650772 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): -75.06100 -13.25200 ymin,ymax (A): 39.09400 98.36600 zmin,zma (A): 7.633000 72.33000 x,y,z range (A): 61.80900 59.27201 64.69700 scale (grids/A): 1.650772 object centre (A): -44.15650 68.73000 39.98150 number of atom coordinates read : 3778 total number of charged atoms : 3648 net assigned charge : 46.00005 assigned positive charge : 596.6970 centred at (gu) : 92.65753 87.47486 84.21175 assigned negative charge : -550.7004 centred at (gu) : 92.33200 87.86357 84.47050 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 81645 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45815 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21168 mr = 45489 m= 2097 mr = 11861 m= 62 mr = 740 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 46881 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 675 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 27923 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) : 0.5502574 object centre at (A) : -44.15650 68.73000 39.98150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1212798E-02 1.7629439E-02 midg,1,midg; midg,igrid,midg 6.3744187E-02 2.8778076E-02 1,midg,midg; igrid,midg,midg 2.2997778E-02 9.3140595E-02 gauss-seidel spectral radius is 0.9983660 estimated iterations to convergence 196 setup time was (sec) 0.7200000 now iterating at: 16:49:40 rms-change max change #iterations 3.924755 164.6972 at 10iterations 1.701302 69.58471 at 20iterations 0.7389835 24.46768 at 30iterations 0.3201757 11.82357 at 40iterations 0.1395358 4.886459 at 50iterations 6.0647894E-02 2.118328 at 60iterations 2.6410643E-02 0.9720516 at 70iterations 1.1544799E-02 0.4012547 at 80iterations 5.0681094E-03 0.1676750 at 90iterations 2.2437563E-03 7.5851440E-02 at 100iterations 1.0051265E-03 3.4135818E-02 at 110iterations 4.6048936E-04 1.5421152E-02 at 120iterations finished qdiffx linear iterations at : 16:49:48 total time elapsed so far: 8.080000 # loops : 120 mean,max change (kT/e) : 4.6048936E-04 1.5421152E-02 energy calculations done at 8.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.210000 DelPhi exited at 16:49:48 8.221u 0.198s 0:08.85 95.0% 0+0k 0+45432io 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 Jan 24 2012 at 16:49:48 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3778 !!! WARNING: CA1 191 has a net charge of 2.0000 !!! WARNING: CA2 192 has a net charge of 2.0000 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: 2.476158 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): -75.06100 -13.25200 ymin,ymax (A): 39.09400 98.36600 zmin,zma (A): 7.633000 72.33000 x,y,z range (A): 61.80900 59.27201 64.69700 scale (grids/A): 2.476158 object centre (A): -44.15650 68.73000 39.98150 number of atom coordinates read : 3778 total number of charged atoms : 3648 net assigned charge : 46.00005 assigned positive charge : 596.6970 centred at (gu) : 93.98593 86.21188 81.31734 assigned negative charge : -550.7004 centred at (gu) : 93.49798 86.79520 81.70568 start vw surface at 0.1300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 188779 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45815 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 73343 mr = 113819 m= 18847 mr = 50968 m= 2863 mr = 11986 m= 145 mr = 1495 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 105676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 29130 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) : 1.650772 object centre at (A) : -44.15650 68.73000 39.98150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9293168 0.2125345 midg,1,midg; midg,igrid,midg 0.7644590 0.4549822 1,midg,midg; igrid,midg,midg 0.2596571 1.483526 gauss-seidel spectral radius is 0.9992585 estimated iterations to convergence 290 setup time was (sec) 1.470000 now iterating at: 16:49:51 rms-change max change #iterations 10.56197 321.3376 at 10iterations 6.382784 166.2346 at 20iterations 3.824352 88.45386 at 30iterations 2.265486 59.12922 at 40iterations 1.332481 34.87460 at 50iterations 0.7811417 19.86508 at 60iterations 0.4567679 9.696810 at 70iterations 0.2668642 5.550757 at 80iterations 0.1553574 3.762043 at 90iterations 8.9937709E-02 1.855457 at 100iterations 5.2295465E-02 1.077721 at 110iterations 3.0194657E-02 0.6420250 at 120iterations 1.7515656E-02 0.3361397 at 130iterations 1.0101358E-02 0.2363663 at 140iterations 5.8385059E-03 0.1182022 at 150iterations 3.3745447E-03 6.3158989E-02 at 160iterations 1.9477801E-03 4.0945053E-02 at 170iterations 1.1245704E-03 2.0854950E-02 at 180iterations finished qdiffx linear iterations at : 16:50:03 total time elapsed so far: 13.28000 # loops : 180 mean,max change (kT/e) : 1.1245704E-03 2.0854950E-02 energy calculations done at 13.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.42000 DelPhi exited at 16:50:03 13.422u 0.217s 0:14.70 92.7% 0+0k 0+45424io 0pf+0w