Mon Oct 10 13:55:34 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 Mon Oct 10 2011 at 13:55:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2852 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: 0.5574957 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): -75.75500 -16.39500 ymin,ymax (A): -45.56900 6.355000 zmin,zma (A): -73.59800 -9.740999 x,y,z range (A): 59.36000 51.92400 63.85700 scale (grids/A): 0.5574957 object centre (A): -46.07500 -19.60700 -41.66950 number of atom coordinates read : 2852 total number of charged atoms : 2700 net assigned charge : 2.000007 assigned positive charge : 415.1539 centred at (gu) : 88.01498 89.03931 91.79703 assigned negative charge : -413.1543 centred at (gu) : 87.84260 89.11928 91.76291 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6235 nv = 96 ne = 84 npr = 53137 no. pairs analyzed = 53137 no. exposed pairs = 4565 no. arc points = 33711 no. surface atoms = 1499 nbur = 1353 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= 288 mr = 2576 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3936 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3319 ## 370 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7791 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4538028E-11 8.2628188E-10 midg,1,midg; midg,igrid,midg 1.2067467E-09 -4.2261297E-10 1,midg,midg; igrid,midg,midg -2.3507813E-09 1.1040839E-09 gauss-seidel spectral radius is 0.9834238 estimated iterations to convergence 64 setup time was (sec) 0.4200000 now iterating at: 13:55:35 rms-change max change #iterations 7.5904034E-02 15.29615 at 10iterations 5.2311355E-03 0.9395118 at 20iterations 3.7131843E-04 5.8934689E-02 at 30iterations 2.5642410E-05 4.3334961E-03 at 40iterations 2.0366799E-06 3.8146973E-04 at 50iterations finished qdiffx linear iterations at : 13:55:38 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 2.0366799E-06 3.8146973E-04 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 13:55:39 3.658u 0.208s 0:04.53 84.9% 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 Mon Oct 10 2011 at 13:55:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2852 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.672487 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): -75.75500 -16.39500 ymin,ymax (A): -45.56900 6.355000 zmin,zma (A): -73.59800 -9.740999 x,y,z range (A): 59.36000 51.92400 63.85700 scale (grids/A): 1.672487 object centre (A): -46.07500 -19.60700 -41.66950 number of atom coordinates read : 2852 total number of charged atoms : 2700 net assigned charge : 2.000007 assigned positive charge : 415.1539 centred at (gu) : 84.04429 87.11714 95.39086 assigned negative charge : -413.1543 centred at (gu) : 83.52755 87.35764 95.28839 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66094 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33711 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20787 mr = 38893 m= 2516 mr = 13040 m= 81 mr = 1067 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 36477 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 294 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 20816 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) : 0.5574957 object centre at (A) : -46.07500 -19.60700 -41.66950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.9159049E-03 2.0787341E-04 midg,1,midg; midg,igrid,midg 1.3595990E-02 3.9948034E-03 1,midg,midg; igrid,midg,midg -9.8528210E-03 1.8109025E-02 gauss-seidel spectral radius is 0.9982949 estimated iterations to convergence 192 setup time was (sec) 0.5900000 now iterating at: 13:55:40 rms-change max change #iterations 3.352238 165.0349 at 10iterations 1.428007 60.47682 at 20iterations 0.6109464 26.87254 at 30iterations 0.2605976 10.36974 at 40iterations 0.1108886 4.194963 at 50iterations 4.7446541E-02 2.163400 at 60iterations 2.0234030E-02 0.7973709 at 70iterations 8.6660003E-03 0.3017702 at 80iterations 3.6876190E-03 0.1295872 at 90iterations 1.5773054E-03 6.0667038E-02 at 100iterations 6.7489361E-04 2.5967121E-02 at 110iterations 2.8910593E-04 1.0633469E-02 at 120iterations finished qdiffx linear iterations at : 13:55:47 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 2.8910593E-04 1.0633469E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 13:55:48 8.031u 0.323s 0:08.99 92.8% 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 13:55:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2852 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.508730 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): -75.75500 -16.39500 ymin,ymax (A): -45.56900 6.355000 zmin,zma (A): -73.59800 -9.740999 x,y,z range (A): 59.36000 51.92400 63.85700 scale (grids/A): 2.508730 object centre (A): -46.07500 -19.60700 -41.66950 number of atom coordinates read : 2852 total number of charged atoms : 2700 net assigned charge : 2.000007 assigned positive charge : 415.1539 centred at (gu) : 81.06635 85.67564 98.08625 assigned negative charge : -413.1543 centred at (gu) : 80.29123 86.03638 97.93245 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 152629 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33711 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67895 mr = 96334 m= 21707 mr = 49971 m= 3740 mr = 15413 m= 288 mr = 2215 m= 5 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 82241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 21592 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) : 1.672487 object centre at (A) : -46.07500 -19.60700 -41.66950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5213328E-02 2.3036100E-02 midg,1,midg; midg,igrid,midg 0.1066275 3.4751225E-02 1,midg,midg; igrid,midg,midg -9.0551421E-02 0.3148565 gauss-seidel spectral radius is 0.9991887 estimated iterations to convergence 277 setup time was (sec) 1.050000 now iterating at: 13:55:49 rms-change max change #iterations 8.971295 303.0167 at 10iterations 5.245116 180.1022 at 20iterations 3.018637 94.26707 at 30iterations 1.728646 50.40120 at 40iterations 0.9846900 26.64152 at 50iterations 0.5595372 12.65990 at 60iterations 0.3158922 10.19424 at 70iterations 0.1779177 4.339264 at 80iterations 0.1004081 2.438643 at 90iterations 5.6229889E-02 1.364372 at 100iterations 3.1660654E-02 0.7628037 at 110iterations 1.7727351E-02 0.3823166 at 120iterations 9.9443989E-03 0.2492766 at 130iterations 5.5672270E-03 0.1331573 at 140iterations 3.1178719E-03 6.6471100E-02 at 150iterations 1.7436274E-03 3.8975298E-02 at 160iterations 9.7735401E-04 2.3851633E-02 at 170iterations 5.4703088E-04 1.2257576E-02 at 180iterations finished qdiffx linear iterations at : 13:56:01 total time elapsed so far: 12.38000 # loops : 180 mean,max change (kT/e) : 5.4703088E-04 1.2257576E-02 energy calculations done at 12.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 13:56:01 12.513u 0.218s 0:13.11 97.0% 0+0k 0+0io 0pf+0w