Mon Oct 10 14:00:06 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 14:00:07 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3456 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5791160 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): -10.93500 50.53800 ymin,ymax (A): -12.61500 42.16500 zmin,zma (A): 17.63700 75.46900 x,y,z range (A): 61.47300 54.78000 57.83200 scale (grids/A): 0.5791160 object centre (A): 19.80150 14.77500 46.55300 number of atom coordinates read : 3456 total number of charged atoms : 3297 net assigned charge : 4.240022 assigned positive charge : 534.5658 centred at (gu) : 90.96178 89.70415 88.08498 assigned negative charge : -530.3271 centred at (gu) : 90.87768 89.79990 88.07333 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7663 nv = 96 ne = 84 npr = 68016 no. pairs analyzed = 68016 no. exposed pairs = 4527 no. arc points = 32151 no. surface atoms = 1527 nbur = 1929 mkacc time = 0.1400000 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 = 1.484000 m= 362 mr = 3862 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3137 ## 315 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9612 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8122243E-10 7.5467760E-10 midg,1,midg; midg,igrid,midg 3.5099179E-09 -1.4759285E-09 1,midg,midg; igrid,midg,midg -1.0142386E-09 3.7460439E-09 gauss-seidel spectral radius is 0.9846523 estimated iterations to convergence 66 setup time was (sec) 0.5800000 now iterating at: 14:00:07 rms-change max change #iterations 0.1038092 14.85872 at 10iterations 8.1618829E-03 1.257921 at 20iterations 7.4129051E-04 0.1090584 at 30iterations 2.0705795E-04 3.1138420E-02 at 40iterations 1.0995464E-04 1.5850067E-02 at 50iterations finished qdiffx linear iterations at : 14:00:10 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 1.0995464E-04 1.5850067E-02 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 14:00:10 3.194u 0.134s 0:03.67 90.4% 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 Mon Oct 10 2011 at 14:00:10 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3456 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.737348 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): -10.93500 50.53800 ymin,ymax (A): -12.61500 42.16500 zmin,zma (A): 17.63700 75.46900 x,y,z range (A): 61.47300 54.78000 57.83200 scale (grids/A): 1.737348 object centre (A): 19.80150 14.77500 46.55300 number of atom coordinates read : 3456 total number of charged atoms : 3297 net assigned charge : 4.240022 assigned positive charge : 534.5658 centred at (gu) : 92.88480 89.11142 84.25391 assigned negative charge : -530.3271 centred at (gu) : 92.63293 89.39945 84.21966 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 83598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32151 grid for indexing accessible points = 1.400000 m= 27411 mr = 56071 m= 3683 mr = 18578 m= 179 mr = 1883 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 38302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 287 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 25551 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) : 0.5791160 object centre at (A) : 19.80150 14.77500 46.55300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4161447E-02 8.2720751E-03 midg,1,midg; midg,igrid,midg 2.3054892E-02 -1.0521321E-02 1,midg,midg; igrid,midg,midg -1.1196982E-02 -1.0841233E-02 gauss-seidel spectral radius is 0.9984545 estimated iterations to convergence 202 setup time was (sec) 0.8400000 now iterating at: 14:00:11 rms-change max change #iterations 4.256048 160.3344 at 10iterations 1.899787 62.89482 at 20iterations 0.8494021 34.19546 at 30iterations 0.3782364 11.04740 at 40iterations 0.1700042 5.394056 at 50iterations 7.6125413E-02 2.551645 at 60iterations 3.4115523E-02 1.082003 at 70iterations 1.5227986E-02 0.5130882 at 80iterations 6.8308269E-03 0.2209282 at 90iterations 3.0617763E-03 9.9138260E-02 at 100iterations 1.3681818E-03 4.3217659E-02 at 110iterations 6.1834161E-04 2.1019936E-02 at 120iterations finished qdiffx linear iterations at : 14:00:17 total time elapsed so far: 6.870000 # loops : 120 mean,max change (kT/e) : 6.1834161E-04 2.1019936E-02 energy calculations done at 6.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 14:00:19 7.105u 0.172s 0:08.47 85.8% 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 14:00:19 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3456 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.606022 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): -10.93500 50.53800 ymin,ymax (A): -12.61500 42.16500 zmin,zma (A): 17.63700 75.46900 x,y,z range (A): 61.47300 54.78000 57.83200 scale (grids/A): 2.606022 object centre (A): 19.80150 14.77500 46.55300 number of atom coordinates read : 3456 total number of charged atoms : 3297 net assigned charge : 4.240022 assigned positive charge : 534.5658 centred at (gu) : 94.32690 88.66702 81.38064 assigned negative charge : -530.3271 centred at (gu) : 93.94932 89.09901 81.32946 start vw surface at 0.2200000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 193921 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32151 grid for indexing accessible points = 1.400000 m= 91844 mr = 137496 m= 29397 mr = 71773 m= 6010 mr = 21801 m= 682 mr = 4030 m= 23 mr = 417 m= 0 mr = 5 time to grow re-entrant surface = 0.8200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.460000 number of dielectric boundary points 86355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 26330 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) : 1.737348 object centre at (A) : 19.80150 14.77500 46.55300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4089056 9.8716132E-02 midg,1,midg; midg,igrid,midg 0.3809582 -0.1415991 1,midg,midg; igrid,midg,midg 1.9196894E-02 -0.5608518 gauss-seidel spectral radius is 0.9992358 estimated iterations to convergence 286 setup time was (sec) 1.740000 now iterating at: 14:00:21 rms-change max change #iterations 10.79488 387.0511 at 10iterations 6.378565 164.2302 at 20iterations 3.723811 89.62637 at 30iterations 2.165893 50.51263 at 40iterations 1.254537 26.52924 at 50iterations 0.7216761 15.26427 at 60iterations 0.4156145 8.859833 at 70iterations 0.2383958 4.767935 at 80iterations 0.1366378 3.067530 at 90iterations 7.8180194E-02 1.704861 at 100iterations 4.4733316E-02 0.9794812 at 110iterations 2.5594098E-02 0.5042591 at 120iterations 1.4591825E-02 0.2683735 at 130iterations 8.3384793E-03 0.1557083 at 140iterations 4.7599287E-03 8.2725525E-02 at 150iterations 2.7139634E-03 5.2875519E-02 at 160iterations 1.5476287E-03 2.7614594E-02 at 170iterations 8.8181079E-04 1.5506983E-02 at 180iterations finished qdiffx linear iterations at : 14:00:30 total time elapsed so far: 11.23000 # loops : 180 mean,max change (kT/e) : 8.8181079E-04 1.5506983E-02 energy calculations done at 11.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.41000 DelPhi exited at 14:00:31 11.410u 0.186s 0:12.02 96.4% 0+0k 0+0io 0pf+0w