Sat Oct 8 20:54:44 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 20:54:44 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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 435 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6195399 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): -31.23000 17.46800 ymin,ymax (A): -23.92800 22.85500 zmin,zma (A): -12.37500 45.08700 x,y,z range (A): 48.69800 46.78300 57.46200 scale (grids/A): 0.6195399 object centre (A): -6.881000 -0.5365000 16.35600 number of atom coordinates read : 2577 total number of charged atoms : 2462 net assigned charge : 4.406007 assigned positive charge : 393.8351 centred at (gu) : 88.52628 89.31674 89.52980 assigned negative charge : -389.4296 centred at (gu) : 88.41639 89.36096 89.41850 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6430 nv = 96 ne = 84 npr = 53300 no. pairs analyzed = 53300 no. exposed pairs = 3001 no. arc points = 21726 no. surface atoms = 1009 nbur = 1568 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 328 mr = 3553 m= 0 mr = 42 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 71 time to turn everything in is 0.2900000 number of dielectric boundary points 3163 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2195 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8037 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2036734E-09 9.7772057E-09 midg,1,midg; midg,igrid,midg 7.5729982E-09 6.3984379E-10 1,midg,midg; igrid,midg,midg -5.2091260E-09 7.7891453E-09 gauss-seidel spectral radius is 0.9865026 estimated iterations to convergence 70 setup time was (sec) 0.5100000 now iterating at: 20:54:45 rms-change max change #iterations 0.1265497 19.18764 at 10iterations 1.1516461E-02 1.911406 at 20iterations 1.0997801E-03 0.1691227 at 30iterations 1.0254981E-04 1.4780045E-02 at 40iterations 1.0675231E-05 1.8138885E-03 at 50iterations finished qdiffx linear iterations at : 20:54:48 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.0675231E-05 1.8138885E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 20:54:48 3.170u 0.172s 0:03.67 91.0% 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 Sat Oct 8 2011 at 20:54:48 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 # of charge parameter records: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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 435 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.858620 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): -31.23000 17.46800 ymin,ymax (A): -23.92800 22.85500 zmin,zma (A): -12.37500 45.08700 x,y,z range (A): 48.69800 46.78300 57.46200 scale (grids/A): 1.858620 object centre (A): -6.881000 -0.5365000 16.35600 number of atom coordinates read : 2577 total number of charged atoms : 2462 net assigned charge : 4.406007 assigned positive charge : 393.8351 centred at (gu) : 85.57836 87.94978 88.58906 assigned negative charge : -389.4296 centred at (gu) : 85.24903 88.08259 88.25535 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21726 grid for indexing accessible points = 1.400000 m= 24309 mr = 48611 m= 3498 mr = 17923 m= 171 mr = 2106 m= 0 mr = 51 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2583 time to turn everything in is 0.5200000 number of dielectric boundary points 29194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 175 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19294 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) : 0.6195399 object centre at (A) : -6.881000 -0.5365000 16.35600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7541820E-02 2.9281853E-02 midg,1,midg; midg,igrid,midg 1.1482689E-02 5.0540280E-04 1,midg,midg; igrid,midg,midg -3.1185423E-03 3.7197407E-02 gauss-seidel spectral radius is 0.9985632 estimated iterations to convergence 209 setup time was (sec) 0.7900000 now iterating at: 20:54:49 rms-change max change #iterations 4.021077 165.1756 at 10iterations 1.848852 66.35492 at 20iterations 0.8477689 29.04794 at 30iterations 0.3892214 12.49558 at 40iterations 0.1792497 6.302711 at 50iterations 8.2300171E-02 2.945046 at 60iterations 3.7779655E-02 1.303963 at 70iterations 1.7330054E-02 0.6282749 at 80iterations 7.9768961E-03 0.2583523 at 90iterations 3.6684477E-03 0.1326075 at 100iterations 1.6772681E-03 5.4347992E-02 at 110iterations 7.7375188E-04 2.5953293E-02 at 120iterations finished qdiffx linear iterations at : 20:54:55 total time elapsed so far: 7.190000 # loops : 120 mean,max change (kT/e) : 7.7375188E-04 2.5953293E-02 energy calculations done at 7.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.370000 DelPhi exited at 20:54:56 7.368u 0.223s 0:07.86 96.4% 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 20:54:56 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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 435 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: 2.787929 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): -31.23000 17.46800 ymin,ymax (A): -23.92800 22.85500 zmin,zma (A): -12.37500 45.08700 x,y,z range (A): 48.69800 46.78300 57.46200 scale (grids/A): 2.787929 object centre (A): -6.881000 -0.5365000 16.35600 number of atom coordinates read : 2577 total number of charged atoms : 2462 net assigned charge : 4.406007 assigned positive charge : 393.8351 centred at (gu) : 83.36744 86.92451 87.88347 assigned negative charge : -389.4296 centred at (gu) : 82.87342 87.12383 87.38286 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 161758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21726 grid for indexing accessible points = 1.400000 m= 79738 mr = 117604 m= 27545 mr = 65504 m= 6299 mr = 22143 m= 763 mr = 4653 m= 26 mr = 488 m= 0 mr = 8 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 8739 time to turn everything in is 1.220000 number of dielectric boundary points 65729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 19695 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) : 1.858620 object centre at (A) : -6.881000 -0.5365000 16.35600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1224826 0.3667648 midg,1,midg; midg,igrid,midg 0.1394017 -1.3274819E-02 1,midg,midg; igrid,midg,midg -5.2956060E-02 0.4968106 gauss-seidel spectral radius is 0.9992329 estimated iterations to convergence 285 setup time was (sec) 1.510000 now iterating at: 20:54:58 rms-change max change #iterations 9.450203 274.0991 at 10iterations 5.428624 115.1741 at 20iterations 3.099355 62.40678 at 30iterations 1.762606 37.88696 at 40iterations 1.004064 19.79516 at 50iterations 0.5721909 11.08488 at 60iterations 0.3257524 6.291020 at 70iterations 0.1851637 3.468526 at 80iterations 0.1054364 2.054406 at 90iterations 5.9860241E-02 1.126465 at 100iterations 3.4048624E-02 0.6890907 at 110iterations 1.9375347E-02 0.3712608 at 120iterations 1.1017262E-02 0.2049561 at 130iterations 6.2627150E-03 0.1188488 at 140iterations 3.5630290E-03 6.8246841E-02 at 150iterations 2.0269095E-03 3.8792610E-02 at 160iterations 1.1583986E-03 2.2920609E-02 at 170iterations 6.6226051E-04 1.2969971E-02 at 180iterations finished qdiffx linear iterations at : 20:55:08 total time elapsed so far: 11.91000 # loops : 180 mean,max change (kT/e) : 6.6226051E-04 1.2969971E-02 energy calculations done at 11.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.09000 DelPhi exited at 20:55:09 12.095u 0.233s 0:12.61 97.7% 0+0k 0+0io 0pf+0w