Tue Oct 11 04:19:42 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 04:19:43 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2714 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6640552 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): -14.78000 32.68800 ymin,ymax (A): 7.659000 55.83000 zmin,zma (A): 25.51300 79.12300 x,y,z range (A): 47.46800 48.17100 53.61000 scale (grids/A): 0.6640552 object centre (A): 8.954000 31.74450 52.31800 number of atom coordinates read : 2714 total number of charged atoms : 2566 net assigned charge : 2.500014 assigned positive charge : 413.2378 centred at (gu) : 90.04045 90.42843 88.55064 assigned negative charge : -410.7383 centred at (gu) : 90.28948 90.24937 88.60514 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8012 nv = 96 ne = 84 npr = 55561 no. pairs analyzed = 55561 no. exposed pairs = 3267 no. arc points = 22687 no. surface atoms = 1106 nbur = 1608 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 448 mr = 4592 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3200000 number of dielectric boundary points 3805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2123 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9377 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6223699E-08 -4.2545225E-09 midg,1,midg; midg,igrid,midg -3.2376693E-08 5.2014538E-08 1,midg,midg; igrid,midg,midg 6.2512107E-08 -5.2899352E-08 gauss-seidel spectral radius is 0.9882521 estimated iterations to convergence 75 setup time was (sec) 0.5600000 now iterating at: 04:19:43 rms-change max change #iterations 0.1782562 24.97346 at 10iterations 1.9447641E-02 2.368749 at 20iterations 2.1600772E-03 0.2681122 at 30iterations 2.6139384E-04 4.1053772E-02 at 40iterations 4.5342786E-05 6.1187744E-03 at 50iterations finished qdiffx linear iterations at : 04:19:46 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 4.5342786E-05 6.1187744E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 04:19:47 3.585u 0.219s 0:04.14 91.5% 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 04:19:47 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2714 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.992166 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): -14.78000 32.68800 ymin,ymax (A): 7.659000 55.83000 zmin,zma (A): 25.51300 79.12300 x,y,z range (A): 47.46800 48.17100 53.61000 scale (grids/A): 1.992166 object centre (A): 8.954000 31.74450 52.31800 number of atom coordinates read : 2714 total number of charged atoms : 2566 net assigned charge : 2.500014 assigned positive charge : 413.2378 centred at (gu) : 90.12069 91.28479 85.65150 assigned negative charge : -410.7383 centred at (gu) : 90.86800 90.74787 85.81500 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 86174 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22687 grid for indexing accessible points = 1.400000 m= 32376 mr = 61412 m= 5263 mr = 24304 m= 360 mr = 3300 m= 7 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 568 time to turn everything in is 0.6700000 number of dielectric boundary points 35026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 20256 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) : 0.6640552 object centre at (A) : 8.954000 31.74450 52.31800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4599873E-03 -3.5298068E-02 midg,1,midg; midg,igrid,midg -1.4278444E-02 3.3750914E-02 1,midg,midg; igrid,midg,midg 7.6915622E-02 -1.8807165E-02 gauss-seidel spectral radius is 0.9987567 estimated iterations to convergence 225 setup time was (sec) 0.9800000 now iterating at: 04:19:48 rms-change max change #iterations 4.822004 202.8319 at 10iterations 2.349941 74.52943 at 20iterations 1.137117 34.57380 at 30iterations 0.5517698 15.85950 at 40iterations 0.2685215 7.588420 at 50iterations 0.1301074 3.826496 at 60iterations 6.3508004E-02 1.895271 at 70iterations 3.0763436E-02 0.8928576 at 80iterations 1.4963903E-02 0.4398794 at 90iterations 7.2665680E-03 0.2141333 at 100iterations 3.5669953E-03 0.1032753 at 110iterations 1.7373658E-03 5.2909136E-02 at 120iterations finished qdiffx linear iterations at : 04:19:56 total time elapsed so far: 8.840000 # loops : 120 mean,max change (kT/e) : 1.7373658E-03 5.2909136E-02 energy calculations done at 8.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.030000 DelPhi exited at 04:19:56 9.034u 0.221s 0:09.62 96.1% 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 Tue Oct 11 2011 at 04:19:56 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2714 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: 2.988248 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): -14.78000 32.68800 ymin,ymax (A): 7.659000 55.83000 zmin,zma (A): 25.51300 79.12300 x,y,z range (A): 47.46800 48.17100 53.61000 scale (grids/A): 2.988248 object centre (A): 8.954000 31.74450 52.31800 number of atom coordinates read : 2714 total number of charged atoms : 2566 net assigned charge : 2.500014 assigned positive charge : 413.2378 centred at (gu) : 90.18085 91.92707 83.47703 assigned negative charge : -410.7383 centred at (gu) : 91.30196 91.12157 83.72253 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 199070 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22687 grid for indexing accessible points = 1.400000 m= 103972 mr = 148102 m= 38811 mr = 86446 m= 9600 mr = 31376 m= 1507 mr = 7171 m= 121 mr = 982 m= 4 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.9999999 no. cavity mid-points inaccessible to solvent = 1921 time to turn everything in is 1.690000 number of dielectric boundary points 78966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 20524 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) : 1.992166 object centre at (A) : 8.954000 31.74450 52.31800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2716774 -0.7078269 midg,1,midg; midg,igrid,midg -0.1355858 0.3823619 1,midg,midg; igrid,midg,midg 0.6500365 -0.1354083 gauss-seidel spectral radius is 0.9992865 estimated iterations to convergence 295 setup time was (sec) 2.040000 now iterating at: 04:19:59 rms-change max change #iterations 11.07223 396.6293 at 10iterations 6.530569 138.2404 at 20iterations 3.831384 71.50081 at 30iterations 2.243758 48.73901 at 40iterations 1.316342 23.12933 at 50iterations 0.7706161 14.02100 at 60iterations 0.4497504 8.664368 at 70iterations 0.2624109 4.271889 at 80iterations 0.1529696 2.757906 at 90iterations 8.9296781E-02 1.588783 at 100iterations 5.2003514E-02 0.8827019 at 110iterations 3.0335231E-02 0.5380912 at 120iterations 1.7683402E-02 0.2887774 at 130iterations 1.0328350E-02 0.1727371 at 140iterations 6.0601244E-03 9.6679688E-02 at 150iterations 3.5676986E-03 6.4132690E-02 at 160iterations 2.1250199E-03 3.7838936E-02 at 170iterations 1.2797016E-03 2.1812439E-02 at 180iterations finished qdiffx linear iterations at : 04:20:10 total time elapsed so far: 13.36000 # loops : 180 mean,max change (kT/e) : 1.2797016E-03 2.1812439E-02 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.59000 DelPhi exited at 04:20:11 13.593u 0.214s 0:14.51 95.1% 0+0k 0+0io 0pf+0w