Thu Jan 26 18:47:01 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 Thu Jan 26 2012 at 18:47:01 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3471 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: 0.5727432 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): -3.077000 48.55300 ymin,ymax (A): -13.31000 48.84700 zmin,zma (A): -4.799000 56.66900 x,y,z range (A): 51.63000 62.15700 61.46800 scale (grids/A): 0.5727432 object centre (A): 22.73800 17.76850 25.93500 number of atom coordinates read : 3471 total number of charged atoms : 3332 net assigned charge : 1.4662743E-05 assigned positive charge : 533.7770 centred at (gu) : 91.33139 88.91510 87.96011 assigned negative charge : -533.7784 centred at (gu) : 91.25562 88.96780 87.94171 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7380 nv = 96 ne = 84 npr = 69596 no. pairs analyzed = 69596 no. exposed pairs = 4379 no. arc points = 30969 no. surface atoms = 1479 nbur = 1992 mkacc time = 0.1500000 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 = 1.512000 m= 297 mr = 3844 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3258 ## 405 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 9637 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6822503E-10 2.1553036E-10 midg,1,midg; midg,igrid,midg 1.3648072E-09 -8.6114110E-10 1,midg,midg; igrid,midg,midg -1.1623886E-09 2.0949682E-09 gauss-seidel spectral radius is 0.9843081 estimated iterations to convergence 66 setup time was (sec) 0.4900000 now iterating at: 18:47:02 rms-change max change #iterations 0.1007812 17.32784 at 10iterations 7.5627170E-03 1.337102 at 20iterations 5.7037611E-04 8.8015556E-02 at 30iterations 4.3838012E-05 6.3362122E-03 at 40iterations 3.3904812E-06 4.9400330E-04 at 50iterations finished qdiffx linear iterations at : 18:47:05 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 3.3904812E-06 4.9400330E-04 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 18:47:06 3.601u 0.179s 0:04.34 86.8% 0+0k 0+46136io 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 Thu Jan 26 2012 at 18:47:06 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 = 3471 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: 1.718230 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): -3.077000 48.55300 ymin,ymax (A): -13.31000 48.84700 zmin,zma (A): -4.799000 56.66900 x,y,z range (A): 51.63000 62.15700 61.46800 scale (grids/A): 1.718230 object centre (A): 22.73800 17.76850 25.93500 number of atom coordinates read : 3471 total number of charged atoms : 3332 net assigned charge : 1.4662743E-05 assigned positive charge : 533.7770 centred at (gu) : 93.99320 86.74438 83.87923 assigned negative charge : -533.7784 centred at (gu) : 93.76624 86.90305 83.82463 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 80961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30969 grid for indexing accessible points = 1.400000 m= 26431 mr = 54605 m= 2969 mr = 18721 m= 97 mr = 1586 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 554 time to turn everything in is 0.5000000 number of dielectric boundary points 35534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 348 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 25782 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) : 0.5727432 object centre at (A) : 22.73800 17.76850 25.93500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6779549E-02 1.4117321E-02 midg,1,midg; midg,igrid,midg 8.9660781E-03 -2.5238183E-03 1,midg,midg; igrid,midg,midg 1.9566854E-03 1.2799896E-03 gauss-seidel spectral radius is 0.9984056 estimated iterations to convergence 199 setup time was (sec) 0.7100000 now iterating at: 18:47:07 rms-change max change #iterations 4.111240 178.5477 at 10iterations 1.798007 68.23840 at 20iterations 0.7914216 24.53525 at 30iterations 0.3482326 11.69600 at 40iterations 0.1535203 5.224556 at 50iterations 6.7326300E-02 2.259830 at 60iterations 2.9737517E-02 0.9713459 at 70iterations 1.3060086E-02 0.4241345 at 80iterations 5.7371645E-03 0.1928759 at 90iterations 2.5296111E-03 8.0699712E-02 at 100iterations 1.1173354E-03 3.5968781E-02 at 110iterations 4.9075624E-04 1.6325951E-02 at 120iterations finished qdiffx linear iterations at : 18:47:15 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 4.9075624E-04 1.6325951E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 18:47:15 8.155u 0.210s 0:09.64 86.7% 0+0k 0+45384io 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 Thu Jan 26 2012 at 18:47:15 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 = 3471 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: 2.577344 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): -3.077000 48.55300 ymin,ymax (A): -13.31000 48.84700 zmin,zma (A): -4.799000 56.66900 x,y,z range (A): 51.63000 62.15700 61.46800 scale (grids/A): 2.577344 object centre (A): 22.73800 17.76850 25.93500 number of atom coordinates read : 3471 total number of charged atoms : 3332 net assigned charge : 1.4662743E-05 assigned positive charge : 533.7770 centred at (gu) : 95.98936 85.11626 80.81860 assigned negative charge : -533.7784 centred at (gu) : 95.64925 85.35442 80.73692 start vw surface at 0.1300000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 187486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30969 grid for indexing accessible points = 1.400000 m= 89460 mr = 133109 m= 27429 mr = 71475 m= 4788 mr = 21240 m= 424 mr = 3320 m= 9 mr = 223 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 1876 time to turn everything in is 1.270000 number of dielectric boundary points 80230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 26647 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) : 1.718230 object centre at (A) : 22.73800 17.76850 25.93500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2623492 0.2105874 midg,1,midg; midg,igrid,midg 0.1586336 3.3655118E-02 1,midg,midg; igrid,midg,midg -6.2076286E-03 -2.3656417E-02 gauss-seidel spectral radius is 0.9992121 estimated iterations to convergence 281 setup time was (sec) 1.510000 now iterating at: 18:47:17 rms-change max change #iterations 10.26139 363.7466 at 10iterations 5.901802 150.2299 at 20iterations 3.368129 63.68965 at 30iterations 1.917460 39.61860 at 40iterations 1.089238 21.08626 at 50iterations 0.6166790 10.75574 at 60iterations 0.3493029 6.596836 at 70iterations 0.1972283 4.120903 at 80iterations 0.1115523 2.497718 at 90iterations 6.2991604E-02 1.156834 at 100iterations 3.5502221E-02 0.7361565 at 110iterations 2.0033725E-02 0.3801270 at 120iterations 1.1285108E-02 0.1893692 at 130iterations 6.3527725E-03 0.1199341 at 140iterations 3.5924485E-03 6.5063953E-02 at 150iterations 2.0243009E-03 3.4719467E-02 at 160iterations 1.1424352E-03 2.2064209E-02 at 170iterations 6.4308592E-04 1.1932373E-02 at 180iterations finished qdiffx linear iterations at : 18:47:29 total time elapsed so far: 13.11000 # loops : 180 mean,max change (kT/e) : 6.4308592E-04 1.1932373E-02 energy calculations done at 13.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.25000 DelPhi exited at 18:47:29 13.260u 0.217s 0:13.94 96.6% 0+0k 0+45376io 0pf+0w