Mon Oct 10 13:55:23 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 13:55:24 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2411 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: 0.6922837 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): -14.43600 36.98800 ymin,ymax (A): -0.4290000 44.33000 zmin,zma (A): -6.457000 43.87400 x,y,z range (A): 51.42400 44.75900 50.33100 scale (grids/A): 0.6922837 object centre (A): 11.27600 21.95050 18.70850 number of atom coordinates read : 2411 total number of charged atoms : 2269 net assigned charge : 3.500024 assigned positive charge : 372.3931 centred at (gu) : 91.08076 91.40222 89.87671 assigned negative charge : -368.8936 centred at (gu) : 91.26318 91.47005 89.83678 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7594 nv = 96 ne = 84 npr = 48270 no. pairs analyzed = 48270 no. exposed pairs = 3136 no. arc points = 21175 no. surface atoms = 1047 nbur = 1364 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 526 mr = 4146 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1974 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8727 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4627911E-09 3.7362238E-08 midg,1,midg; midg,igrid,midg 3.7677598E-08 -8.8335783E-09 1,midg,midg; igrid,midg,midg 7.7152158E-08 -6.8673963E-08 gauss-seidel spectral radius is 0.9891593 estimated iterations to convergence 78 setup time was (sec) 0.3800000 now iterating at: 13:55:24 rms-change max change #iterations 0.2033767 27.79930 at 10iterations 2.4235602E-02 3.314758 at 20iterations 3.0381051E-03 0.4242899 at 30iterations 5.2889012E-04 7.7182770E-02 at 40iterations 1.3922573E-04 1.9508362E-02 at 50iterations finished qdiffx linear iterations at : 13:55:27 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.3922573E-04 1.9508362E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 13:55:27 3.355u 0.172s 0:03.82 92.1% 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 13:55:27 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2411 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: 2.076851 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): -14.43600 36.98800 ymin,ymax (A): -0.4290000 44.33000 zmin,zma (A): -6.457000 43.87400 x,y,z range (A): 51.42400 44.75900 50.33100 scale (grids/A): 2.076851 object centre (A): 11.27600 21.95050 18.70850 number of atom coordinates read : 2411 total number of charged atoms : 2269 net assigned charge : 3.500024 assigned positive charge : 372.3931 centred at (gu) : 93.24194 94.20621 89.62991 assigned negative charge : -368.8936 centred at (gu) : 93.78938 94.41006 89.51019 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21175 grid for indexing accessible points = 1.400000 m= 31701 mr = 55355 m= 6260 mr = 23541 m= 625 mr = 4189 m= 12 mr = 327 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 35605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 17992 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) : 0.6922837 object centre at (A) : 11.27600 21.95050 18.70850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1379007E-02 1.5125538E-02 midg,1,midg; midg,igrid,midg 3.4918010E-02 2.9885264E-03 1,midg,midg; igrid,midg,midg 1.6149353E-02 -7.0731662E-02 gauss-seidel spectral radius is 0.9988225 estimated iterations to convergence 231 setup time was (sec) 0.6300000 now iterating at: 13:55:28 rms-change max change #iterations 4.970415 214.5517 at 10iterations 2.450539 93.31981 at 20iterations 1.213619 44.98392 at 30iterations 0.5997187 19.03301 at 40iterations 0.2968683 8.182549 at 50iterations 0.1474615 4.414347 at 60iterations 7.3014855E-02 2.108658 at 70iterations 3.6260087E-02 1.086607 at 80iterations 1.8033652E-02 0.4960194 at 90iterations 9.0188719E-03 0.2467394 at 100iterations 4.5424975E-03 0.1248531 at 110iterations 2.3446453E-03 6.8615913E-02 at 120iterations finished qdiffx linear iterations at : 13:55:35 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 2.3446453E-03 6.8615913E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 13:55:36 7.941u 0.190s 0:08.60 94.5% 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 13:55:36 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2411 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: 3.115277 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): -14.43600 36.98800 ymin,ymax (A): -0.4290000 44.33000 zmin,zma (A): -6.457000 43.87400 x,y,z range (A): 51.42400 44.75900 50.33100 scale (grids/A): 3.115277 object centre (A): 11.27600 21.95050 18.70850 number of atom coordinates read : 2411 total number of charged atoms : 2269 net assigned charge : 3.500024 assigned positive charge : 372.3931 centred at (gu) : 94.86267 96.30910 89.44474 assigned negative charge : -368.8936 centred at (gu) : 95.68401 96.61504 89.26507 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 185245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21175 grid for indexing accessible points = 1.400000 m= 98045 mr = 133625 m= 40591 mr = 80212 m= 11934 mr = 33132 m= 2601 mr = 9285 m= 338 mr = 1955 m= 21 mr = 209 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.260000 number of dielectric boundary points 80353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 18152 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) : 2.076851 object centre at (A) : 11.27600 21.95050 18.70850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2743592 4.1379388E-02 midg,1,midg; midg,igrid,midg 0.3045869 -9.7812533E-02 1,midg,midg; igrid,midg,midg 0.3433419 -0.6678244 gauss-seidel spectral radius is 0.9992990 estimated iterations to convergence 298 setup time was (sec) 1.510000 now iterating at: 13:55:38 rms-change max change #iterations 11.14105 460.6796 at 10iterations 6.626817 126.7046 at 20iterations 3.916853 79.59744 at 30iterations 2.313165 42.59729 at 40iterations 1.364632 22.89522 at 50iterations 0.8020240 15.95411 at 60iterations 0.4710785 8.434838 at 70iterations 0.2762546 4.330752 at 80iterations 0.1619741 2.824684 at 90iterations 9.4867989E-02 1.624153 at 100iterations 5.5719532E-02 1.045723 at 110iterations 3.2836150E-02 0.5902017 at 120iterations 1.9291891E-02 0.3430796 at 130iterations 1.1527994E-02 0.2048454 at 140iterations 6.9606751E-03 0.1523895 at 150iterations 4.3336414E-03 8.7299347E-02 at 160iterations 2.8188857E-03 6.0235977E-02 at 170iterations 1.9418148E-03 4.3762207E-02 at 180iterations finished qdiffx linear iterations at : 13:55:49 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 1.9418148E-03 4.3762207E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 13:55:50 13.085u 0.243s 0:13.66 97.5% 0+0k 0+0io 0pf+0w