Mon Oct 10 21:31:52 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 Mon Oct 10 2011 at 21:31:52 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2814 !!! WARNING: GLM 44 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5588346 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): 0.1200000 54.75600 ymin,ymax (A): -33.33700 23.75800 zmin,zma (A): -22.51900 41.18500 x,y,z range (A): 54.63600 57.09500 63.70400 scale (grids/A): 0.5588346 object centre (A): 27.43800 -4.789498 9.333000 number of atom coordinates read : 2814 total number of charged atoms : 2735 net assigned charge : 2.406007 assigned positive charge : 417.0432 centred at (gu) : 87.31048 88.90524 89.07443 assigned negative charge : -414.6385 centred at (gu) : 87.40340 88.99329 89.11887 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5866 nv = 96 ne = 84 npr = 54491 no. pairs analyzed = 54491 no. exposed pairs = 4001 no. arc points = 27996 no. surface atoms = 1350 nbur = 1464 mkacc time = 8.9999996E-02 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 = 1.540000 m= 267 mr = 2766 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2848 ## 324 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.9406681E-10 -1.8749323E-10 midg,1,midg; midg,igrid,midg 1.3796838E-09 -5.1200422E-10 1,midg,midg; igrid,midg,midg 2.1458213E-09 -3.7169326E-10 gauss-seidel spectral radius is 0.9834816 estimated iterations to convergence 64 setup time was (sec) 0.3900000 now iterating at: 21:31:53 rms-change max change #iterations 7.7125520E-02 14.10375 at 10iterations 5.4651895E-03 1.033716 at 20iterations 4.5586409E-04 6.7577362E-02 at 30iterations 7.0419708E-05 9.9716187E-03 at 40iterations 1.7270904E-05 2.2664070E-03 at 50iterations finished qdiffx linear iterations at : 21:31:55 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.7270904E-05 2.2664070E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 21:31:56 3.380u 0.170s 0:04.39 80.8% 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 Mon Oct 10 2011 at 21:31:56 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2814 !!! WARNING: GLM 44 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.676504 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): 0.1200000 54.75600 ymin,ymax (A): -33.33700 23.75800 zmin,zma (A): -22.51900 41.18500 x,y,z range (A): 54.63600 57.09500 63.70400 scale (grids/A): 1.676504 object centre (A): 27.43800 -4.789498 9.333000 number of atom coordinates read : 2814 total number of charged atoms : 2735 net assigned charge : 2.406007 assigned positive charge : 417.0432 centred at (gu) : 81.93061 86.71500 87.22240 assigned negative charge : -414.6385 centred at (gu) : 82.21009 86.97966 87.35636 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63762 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27996 grid for indexing accessible points = 1.400000 m= 20542 mr = 40835 m= 2546 mr = 13749 m= 69 mr = 1280 m= 0 mr = 9 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.3300000 number of dielectric boundary points 31046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 267 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 21057 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) : 0.5588346 object centre at (A) : 27.43800 -4.789498 9.333000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4846973E-03 -1.0824124E-02 midg,1,midg; midg,igrid,midg 1.4204554E-03 -8.6830826E-03 1,midg,midg; igrid,midg,midg 2.9682729E-02 3.4326592E-03 gauss-seidel spectral radius is 0.9982731 estimated iterations to convergence 191 setup time was (sec) 0.5400000 now iterating at: 21:31:57 rms-change max change #iterations 3.376621 192.8519 at 10iterations 1.432706 56.98457 at 20iterations 0.6085118 22.30518 at 30iterations 0.2585503 9.476784 at 40iterations 0.1098453 4.542331 at 50iterations 4.6725411E-02 1.762701 at 60iterations 1.9840639E-02 0.6822815 at 70iterations 8.4898723E-03 0.3445358 at 80iterations 3.6317236E-03 0.1350546 at 90iterations 1.5501273E-03 5.5976868E-02 at 100iterations 6.6764187E-04 2.4672508E-02 at 110iterations 2.9224434E-04 1.0805607E-02 at 120iterations finished qdiffx linear iterations at : 21:32:04 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 2.9224434E-04 1.0805607E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 21:32:05 7.671u 0.201s 0:08.40 93.6% 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 Mon Oct 10 2011 at 21:32:05 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2814 !!! WARNING: GLM 44 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.514756 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): 0.1200000 54.75600 ymin,ymax (A): -33.33700 23.75800 zmin,zma (A): -22.51900 41.18500 x,y,z range (A): 54.63600 57.09500 63.70400 scale (grids/A): 2.514756 object centre (A): 27.43800 -4.789498 9.333000 number of atom coordinates read : 2814 total number of charged atoms : 2735 net assigned charge : 2.406007 assigned positive charge : 417.0432 centred at (gu) : 77.89568 85.07230 85.83351 assigned negative charge : -414.6385 centred at (gu) : 78.31500 85.46935 86.03442 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 147927 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27996 grid for indexing accessible points = 1.400000 m= 67964 mr = 100562 m= 21817 mr = 52173 m= 4098 mr = 16474 m= 288 mr = 2748 m= 5 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 168 time to turn everything in is 0.7900000 number of dielectric boundary points 70026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 21853 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) : 1.676504 object centre at (A) : 27.43800 -4.789498 9.333000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1679058 -0.1776573 midg,1,midg; midg,igrid,midg -5.0957203E-02 -0.1241885 1,midg,midg; igrid,midg,midg 0.3923813 6.5273099E-02 gauss-seidel spectral radius is 0.9991664 estimated iterations to convergence 274 setup time was (sec) 1.010000 now iterating at: 21:32:06 rms-change max change #iterations 8.754635 286.5568 at 10iterations 5.013944 118.1162 at 20iterations 2.847404 74.55331 at 30iterations 1.606970 42.72622 at 40iterations 0.9038568 18.97579 at 50iterations 0.5065293 10.96590 at 60iterations 0.2831965 6.005234 at 70iterations 0.1575444 3.289267 at 80iterations 8.8108078E-02 1.976827 at 90iterations 4.9115494E-02 1.132674 at 100iterations 2.7268698E-02 0.5826740 at 110iterations 1.5157667E-02 0.3266020 at 120iterations 8.4366128E-03 0.1659527 at 130iterations 4.6962518E-03 0.1026821 at 140iterations 2.5974810E-03 5.5904388E-02 at 150iterations 1.4481815E-03 2.9389381E-02 at 160iterations 8.0523087E-04 1.6288280E-02 at 170iterations 4.4802509E-04 9.8313093E-03 at 180iterations finished qdiffx linear iterations at : 21:32:17 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 4.4802509E-04 9.8313093E-03 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 21:32:18 12.346u 0.234s 0:13.16 95.5% 0+0k 0+0io 0pf+0w