Sat Oct 8 19:32:25 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 Sat Oct 8 2011 at 19:32:25 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 443 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.7038494 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): -5.822000 43.78000 ymin,ymax (A): -3.035000 47.54400 zmin,zma (A): -8.311000 40.47800 x,y,z range (A): 49.60200 50.57900 48.78900 scale (grids/A): 0.7038494 object centre (A): 18.97900 22.25450 16.08350 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.200010 assigned positive charge : 393.3950 centred at (gu) : 88.43716 92.05309 90.60526 assigned negative charge : -389.1955 centred at (gu) : 88.30434 92.14962 90.55128 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8786 nv = 96 ne = 84 npr = 54553 no. pairs analyzed = 54553 no. exposed pairs = 3021 no. arc points = 21579 no. surface atoms = 1011 nbur = 1595 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 605 mr = 5123 m= 4 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 266 time to turn everything in is 0.3300000 number of dielectric boundary points 4131 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2040 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9838 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8682404E-09 7.3241004E-08 midg,1,midg; midg,igrid,midg 5.9609576E-08 -3.1969343E-08 1,midg,midg; igrid,midg,midg -5.7418518E-08 8.0171844E-08 gauss-seidel spectral radius is 0.9895312 estimated iterations to convergence 80 setup time was (sec) 0.5700000 now iterating at: 19:32:26 rms-change max change #iterations 0.2222584 33.81900 at 10iterations 2.7410479E-02 3.683090 at 20iterations 3.3779454E-03 0.4854870 at 30iterations 4.0837069E-04 6.4093590E-02 at 40iterations 5.0533996E-05 6.4096451E-03 at 50iterations finished qdiffx linear iterations at : 19:32:28 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 5.0533996E-05 6.4096451E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 19:32:29 3.323u 0.184s 0:03.79 92.3% 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 Sat Oct 8 2011 at 19:32:29 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 443 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.111548 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): -5.822000 43.78000 ymin,ymax (A): -3.035000 47.54400 zmin,zma (A): -8.311000 40.47800 x,y,z range (A): 49.60200 50.57900 48.78900 scale (grids/A): 2.111548 object centre (A): 18.97900 22.25450 16.08350 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.200010 assigned positive charge : 393.3950 centred at (gu) : 85.31101 96.15909 91.81537 assigned negative charge : -389.1955 centred at (gu) : 84.91283 96.44865 91.65352 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 92525 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21579 grid for indexing accessible points = 1.400000 m= 37794 mr = 65676 m= 8024 mr = 29495 m= 768 mr = 5714 m= 12 mr = 399 m= 0 mr = 2 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 8419 time to turn everything in is 0.6800000 number of dielectric boundary points 37837 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 19563 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) : 0.7038494 object centre at (A) : 18.97900 22.25450 16.08350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4164889E-03 1.8446136E-02 midg,1,midg; midg,igrid,midg 8.9407042E-03 -2.2670997E-02 1,midg,midg; igrid,midg,midg -1.2023184E-02 0.1002308 gauss-seidel spectral radius is 0.9988685 estimated iterations to convergence 235 setup time was (sec) 0.9700000 now iterating at: 19:32:30 rms-change max change #iterations 5.207828 208.7011 at 10iterations 2.583564 88.99446 at 20iterations 1.295871 40.00792 at 30iterations 0.6493400 17.01253 at 40iterations 0.3259416 9.135483 at 50iterations 0.1631839 4.293433 at 60iterations 8.1946038E-02 2.553244 at 70iterations 4.1109029E-02 1.120953 at 80iterations 2.0607548E-02 0.5602031 at 90iterations 1.0318057E-02 0.2842560 at 100iterations 5.1849722E-03 0.1452274 at 110iterations 2.5983099E-03 6.6635132E-02 at 120iterations finished qdiffx linear iterations at : 19:32:38 total time elapsed so far: 8.360000 # loops : 120 mean,max change (kT/e) : 2.5983099E-03 6.6635132E-02 energy calculations done at 8.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.530000 DelPhi exited at 19:32:38 8.532u 0.239s 0:09.04 96.9% 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 Sat Oct 8 2011 at 19:32:38 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 443 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.167322 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): -5.822000 43.78000 ymin,ymax (A): -3.035000 47.54400 zmin,zma (A): -8.311000 40.47800 x,y,z range (A): 49.60200 50.57900 48.78900 scale (grids/A): 3.167322 object centre (A): 18.97900 22.25450 16.08350 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.200010 assigned positive charge : 393.3950 centred at (gu) : 82.96635 99.23848 92.72287 assigned negative charge : -389.1955 centred at (gu) : 82.36919 99.67286 92.48021 start vw surface at 0.1300000 fill in re-entrant regions at 0.9400000 boundary points on vw surface= 213261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21579 grid for indexing accessible points = 1.400000 m= 116550 mr = 157891 m= 49816 mr = 98444 m= 15359 mr = 41936 m= 3418 mr = 12454 m= 407 mr = 2618 m= 16 mr = 272 m= 0 mr = 3 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 28071 time to turn everything in is 2.090000 number of dielectric boundary points 85209 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.240000 number of grid points assigned charge 19728 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) : 2.111548 object centre at (A) : 18.97900 22.25450 16.08350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2982371 0.1568826 midg,1,midg; midg,igrid,midg 1.9836612E-02 -0.1873001 1,midg,midg; igrid,midg,midg -0.1620879 1.431359 gauss-seidel spectral radius is 0.9993131 estimated iterations to convergence 301 setup time was (sec) 2.410000 now iterating at: 19:32:41 rms-change max change #iterations 11.41897 328.4024 at 10iterations 6.698387 115.9757 at 20iterations 3.943995 64.23468 at 30iterations 2.310347 36.26717 at 40iterations 1.360651 22.39211 at 50iterations 0.7981571 11.57390 at 60iterations 0.4685788 8.153660 at 70iterations 0.2750967 4.432727 at 80iterations 0.1610837 2.494649 at 90iterations 9.4386734E-02 1.446936 at 100iterations 5.5458192E-02 1.016517 at 110iterations 3.2449171E-02 0.5092545 at 120iterations 1.9068761E-02 0.3246002 at 130iterations 1.1183457E-02 0.1803598 at 140iterations 6.5661827E-03 0.1115732 at 150iterations 3.8403387E-03 6.9554567E-02 at 160iterations 2.2567147E-03 3.5655975E-02 at 170iterations 1.3215119E-03 2.1032333E-02 at 180iterations finished qdiffx linear iterations at : 19:32:51 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 1.3215119E-03 2.1032333E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 19:32:52 13.233u 0.216s 0:13.70 98.1% 0+0k 0+0io 0pf+0w