Sat Oct 8 11:37:50 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+sph2.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 = amb2.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 11:37:50 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3314 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: 0.6223668 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): 32.87300 80.13400 ymin,ymax (A): 24.25300 81.45399 zmin,zma (A): -2.299000 46.17900 x,y,z range (A): 47.26101 57.20100 48.47800 scale (grids/A): 0.6223668 object centre (A): 56.50350 52.85350 21.94000 number of atom coordinates read : 3314 total number of charged atoms : 3164 net assigned charge : -3.499974 assigned positive charge : 504.4564 centred at (gu) : 90.67970 89.90910 90.79668 assigned negative charge : -507.9576 centred at (gu) : 90.46625 89.98459 90.78139 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8169 nv = 96 ne = 84 npr = 70415 no. pairs analyzed = 70415 no. exposed pairs = 3776 no. arc points = 25491 no. surface atoms = 1278 nbur = 2036 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 435 mr = 4837 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 60 time to turn everything in is 0.3400000 number of dielectric boundary points 3729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2452 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 10240 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8742920E-09 -2.0591333E-09 midg,1,midg; midg,igrid,midg 3.8814174E-09 -1.0058856E-08 1,midg,midg; igrid,midg,midg -2.0244714E-08 1.8948326E-08 gauss-seidel spectral radius is 0.9866779 estimated iterations to convergence 71 setup time was (sec) 0.5600000 now iterating at: 11:37:51 rms-change max change #iterations 0.1527483 21.86814 at 10iterations 1.4208991E-02 2.303432 at 20iterations 1.3552121E-03 0.1617451 at 30iterations 1.2905699E-04 1.6239166E-02 at 40iterations 1.3341041E-05 1.8501282E-03 at 50iterations finished qdiffx linear iterations at : 11:37:53 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 1.3341041E-05 1.8501282E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 11:37:54 3.133u 0.142s 0:03.83 85.3% 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 11:37:54 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3314 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: 1.867100 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): 32.87300 80.13400 ymin,ymax (A): 24.25300 81.45399 zmin,zma (A): -2.299000 46.17900 x,y,z range (A): 47.26101 57.20100 48.47800 scale (grids/A): 1.867100 object centre (A): 56.50350 52.85350 21.94000 number of atom coordinates read : 3314 total number of charged atoms : 3164 net assigned charge : -3.499974 assigned positive charge : 504.4564 centred at (gu) : 92.03819 89.72666 92.38894 assigned negative charge : -507.9576 centred at (gu) : 91.39797 89.95319 92.34381 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 88442 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25491 grid for indexing accessible points = 1.400000 m= 33800 mr = 63533 m= 5747 mr = 26077 m= 284 mr = 3835 m= 1 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 4641 time to turn everything in is 0.6100000 number of dielectric boundary points 34746 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 24825 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) : 0.6223668 object centre at (A) : 56.50350 52.85350 21.94000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7038733E-02 -3.2388691E-02 midg,1,midg; midg,igrid,midg 1.0396228E-02 -2.8946906E-02 1,midg,midg; igrid,midg,midg -2.8117163E-02 3.0959081E-02 gauss-seidel spectral radius is 0.9986368 estimated iterations to convergence 215 setup time was (sec) 0.8600000 now iterating at: 11:37:55 rms-change max change #iterations 4.746697 183.4509 at 10iterations 2.217598 66.33582 at 20iterations 1.040571 33.49419 at 30iterations 0.4889921 14.59986 at 40iterations 0.2297976 7.539558 at 50iterations 0.1077648 3.446036 at 60iterations 5.0368700E-02 1.460159 at 70iterations 2.3718322E-02 0.6544056 at 80iterations 1.1163050E-02 0.3372211 at 90iterations 5.2171480E-03 0.1575851 at 100iterations 2.4616532E-03 7.0931435E-02 at 110iterations 1.1541715E-03 3.2598019E-02 at 120iterations finished qdiffx linear iterations at : 11:38:01 total time elapsed so far: 6.770000 # loops : 120 mean,max change (kT/e) : 1.1541715E-03 3.2598019E-02 energy calculations done at 6.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.940000 DelPhi exited at 11:38:01 6.947u 0.170s 0:07.41 95.9% 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 11:38:01 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3314 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: 2.800651 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): 32.87300 80.13400 ymin,ymax (A): 24.25300 81.45399 zmin,zma (A): -2.299000 46.17900 x,y,z range (A): 47.26101 57.20100 48.47800 scale (grids/A): 2.800651 object centre (A): 56.50350 52.85350 21.94000 number of atom coordinates read : 3314 total number of charged atoms : 3164 net assigned charge : -3.499974 assigned positive charge : 504.4564 centred at (gu) : 93.05709 89.58987 93.58318 assigned negative charge : -507.9576 centred at (gu) : 92.09698 89.92963 93.51565 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 205021 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25491 grid for indexing accessible points = 1.400000 m= 107441 mr = 153888 m= 41995 mr = 89926 m= 10470 mr = 35062 m= 1393 mr = 8170 m= 60 mr = 1010 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 15501 time to turn everything in is 1.510000 number of dielectric boundary points 78307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 25312 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) : 1.867100 object centre at (A) : 56.50350 52.85350 21.94000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2510046 -0.3367260 midg,1,midg; midg,igrid,midg 5.0557885E-02 -5.9448555E-02 1,midg,midg; igrid,midg,midg -0.2853603 0.3309427 gauss-seidel spectral radius is 0.9992623 estimated iterations to convergence 291 setup time was (sec) 1.800000 now iterating at: 11:38:03 rms-change max change #iterations 11.06874 320.0570 at 10iterations 6.483378 129.8835 at 20iterations 3.753191 69.42844 at 30iterations 2.183102 41.13346 at 40iterations 1.261325 25.22647 at 50iterations 0.7286679 14.06743 at 60iterations 0.4199033 6.649869 at 70iterations 0.2421893 5.083853 at 80iterations 0.1394873 2.442817 at 90iterations 8.0426164E-02 1.266266 at 100iterations 4.6169765E-02 0.7605419 at 110iterations 2.6617061E-02 0.4471359 at 120iterations 1.5318248E-02 0.2637707 at 130iterations 8.8204397E-03 0.1414385 at 140iterations 5.0708456E-03 8.2508087E-02 at 150iterations 2.9263140E-03 4.8059464E-02 at 160iterations 1.6862771E-03 2.8181076E-02 at 170iterations 9.7149337E-04 1.7852783E-02 at 180iterations finished qdiffx linear iterations at : 11:38:13 total time elapsed so far: 11.33000 # loops : 180 mean,max change (kT/e) : 9.7149337E-04 1.7852783E-02 energy calculations done at 11.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.50000 DelPhi exited at 11:38:14 11.503u 0.175s 0:12.36 94.4% 0+0k 0+0io 0pf+0w