Tue Oct 11 06:24:20 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 Tue Oct 11 2011 at 06:24:20 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1330 !!! WARNING: SEP 98 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.8050474 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): -14.73700 25.58900 ymin,ymax (A): 40.12400 76.44600 zmin,zma (A): -4.722000 39.49900 x,y,z range (A): 40.32600 36.32200 44.22100 scale (grids/A): 0.8050474 object centre (A): 5.426001 58.28500 17.38850 number of atom coordinates read : 1330 total number of charged atoms : 1266 net assigned charge : 2.025002 assigned positive charge : 202.5574 centred at (gu) : 90.02071 90.87933 89.84326 assigned negative charge : -200.5323 centred at (gu) : 90.14272 90.91987 89.55182 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6466 nv = 96 ne = 84 npr = 24771 no. pairs analyzed = 24771 no. exposed pairs = 1727 no. arc points = 12382 no. surface atoms = 598 nbur = 732 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 544 mr = 3673 m= 7 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1200000 number of dielectric boundary points 3227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 883 ## 79 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 6050 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2539576E-07 7.2569247E-07 midg,1,midg; midg,igrid,midg 1.9029430E-07 5.2629325E-08 1,midg,midg; igrid,midg,midg 3.9264350E-07 -1.3227397E-07 gauss-seidel spectral radius is 0.9918749 estimated iterations to convergence 90 setup time was (sec) 0.3200000 now iterating at: 06:24:20 rms-change max change #iterations 0.2763034 36.75459 at 10iterations 4.2852055E-02 5.532531 at 20iterations 6.7933840E-03 0.8692535 at 30iterations 1.1162104E-03 0.1492796 at 40iterations 2.2059622E-04 2.9291868E-02 at 50iterations finished qdiffx linear iterations at : 06:24:23 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 2.2059622E-04 2.9291868E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 06:24:24 3.364u 0.194s 0:03.87 91.7% 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 Tue Oct 11 2011 at 06:24:24 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1330 !!! WARNING: SEP 98 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.415142 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): -14.73700 25.58900 ymin,ymax (A): 40.12400 76.44600 zmin,zma (A): -4.722000 39.49900 x,y,z range (A): 40.32600 36.32200 44.22100 scale (grids/A): 2.415142 object centre (A): 5.426001 58.28500 17.38850 number of atom coordinates read : 1330 total number of charged atoms : 1266 net assigned charge : 2.025002 assigned positive charge : 202.5574 centred at (gu) : 90.06268 92.63837 89.53011 assigned negative charge : -200.5323 centred at (gu) : 90.42860 92.75987 88.65569 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 67006 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12382 grid for indexing accessible points = 1.400000 m= 29868 mr = 46806 m= 7758 mr = 23259 m= 1024 mr = 5640 m= 52 mr = 585 m= 0 mr = 11 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 29407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 10113 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) : 0.8050474 object centre at (A) : 5.426001 58.28500 17.38850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4010569E-02 7.4299932E-02 midg,1,midg; midg,igrid,midg 7.3074149E-03 4.8720632E-03 1,midg,midg; igrid,midg,midg 7.2824530E-02 1.5345054E-02 gauss-seidel spectral radius is 0.9989998 estimated iterations to convergence 250 setup time was (sec) 0.5700000 now iterating at: 06:24:25 rms-change max change #iterations 4.584579 209.0332 at 10iterations 2.400828 78.48138 at 20iterations 1.258901 38.50473 at 30iterations 0.6566126 20.03642 at 40iterations 0.3429088 10.12965 at 50iterations 0.1799200 5.523026 at 60iterations 9.3839332E-02 2.952719 at 70iterations 4.9172923E-02 1.618497 at 80iterations 2.5712738E-02 0.8065357 at 90iterations 1.3586264E-02 0.3972015 at 100iterations 7.2028656E-03 0.2142334 at 110iterations 3.8809867E-03 0.1245193 at 120iterations finished qdiffx linear iterations at : 06:24:32 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 3.8809867E-03 0.1245193 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 06:24:32 7.905u 0.217s 0:08.40 96.5% 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 Tue Oct 11 2011 at 06:24:32 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1330 !!! WARNING: SEP 98 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.622713 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): -14.73700 25.58900 ymin,ymax (A): 40.12400 76.44600 zmin,zma (A): -4.722000 39.49900 x,y,z range (A): 40.32600 36.32200 44.22100 scale (grids/A): 3.622713 object centre (A): 5.426001 58.28500 17.38850 number of atom coordinates read : 1330 total number of charged atoms : 1266 net assigned charge : 2.025002 assigned positive charge : 202.5574 centred at (gu) : 90.09413 93.95769 89.29527 assigned negative charge : -200.5323 centred at (gu) : 90.64307 94.13987 87.98355 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 153952 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12382 grid for indexing accessible points = 1.400000 m= 87657 mr = 112223 m= 42063 mr = 73674 m= 15507 mr = 35627 m= 4066 mr = 12594 m= 700 mr = 3092 m= 78 mr = 457 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 66316 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 10128 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) : 2.415142 object centre at (A) : 5.426001 58.28500 17.38850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6870278 0.4911272 midg,1,midg; midg,igrid,midg 3.4331903E-02 4.5042317E-02 1,midg,midg; igrid,midg,midg 0.5102955 4.7020856E-02 gauss-seidel spectral radius is 0.9993288 estimated iterations to convergence 304 setup time was (sec) 1.340000 now iterating at: 06:24:34 rms-change max change #iterations 9.750229 285.3847 at 10iterations 5.900759 140.5048 at 20iterations 3.543827 83.82982 at 30iterations 2.130668 48.83018 at 40iterations 1.271350 32.31615 at 50iterations 0.7605072 14.38815 at 60iterations 0.4517765 9.190205 at 70iterations 0.2686836 5.372374 at 80iterations 0.1600678 2.858833 at 90iterations 9.5009215E-02 2.062899 at 100iterations 5.6342315E-02 1.042224 at 110iterations 3.3387605E-02 0.5741911 at 120iterations 1.9810217E-02 0.3746221 at 130iterations 1.1775413E-02 0.2188530 at 140iterations 7.0022452E-03 0.1265001 at 150iterations 4.1802400E-03 8.0642700E-02 at 160iterations 2.5299527E-03 4.7523499E-02 at 170iterations 1.5603026E-03 3.4957886E-02 at 180iterations finished qdiffx linear iterations at : 06:24:45 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 1.5603026E-03 3.4957886E-02 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 06:24:46 12.948u 0.216s 0:13.72 95.8% 0+0k 0+0io 0pf+0w