Tue Oct 11 06:13:22 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 Tue Oct 11 2011 at 06:13:23 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 = 2037 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: 0.7044204 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): 27.12100 70.64700 ymin,ymax (A): 43.92200 81.20200 zmin,zma (A): -60.25700 -9.719001 x,y,z range (A): 43.52600 37.28001 50.53800 scale (grids/A): 0.7044204 object centre (A): 48.88400 62.56200 -34.98800 number of atom coordinates read : 2037 total number of charged atoms : 1912 net assigned charge : 6.500010 assigned positive charge : 308.6971 centred at (gu) : 90.61224 89.70490 89.04755 assigned negative charge : -302.1972 centred at (gu) : 90.78507 89.75086 89.05561 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6976 nv = 96 ne = 84 npr = 40244 no. pairs analyzed = 40244 no. exposed pairs = 2595 no. arc points = 17639 no. surface atoms = 881 nbur = 1156 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 477 mr = 3942 m= 2 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1569 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 7611 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6067592E-08 4.0082863E-08 midg,1,midg; midg,igrid,midg 7.6154443E-08 2.9253705E-08 1,midg,midg; igrid,midg,midg 1.1310982E-07 -3.1120567E-08 gauss-seidel spectral radius is 0.9894939 estimated iterations to convergence 79 setup time was (sec) 0.5000000 now iterating at: 06:13:23 rms-change max change #iterations 0.1947060 27.27716 at 10iterations 2.4422422E-02 3.345377 at 20iterations 3.2798266E-03 0.5581570 at 30iterations 6.4963504E-04 7.3732376E-02 at 40iterations 1.9192295E-04 2.1460533E-02 at 50iterations finished qdiffx linear iterations at : 06:13:27 total time elapsed so far: 4.200000 # loops : 50 mean,max change (kT/e) : 1.9192295E-04 2.1460533E-02 energy calculations done at 4.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 06:13:28 4.378u 0.402s 0:05.18 92.0% 0+0k 0+0io 6pf+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 06:13:28 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 = 2037 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: 2.113261 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): 27.12100 70.64700 ymin,ymax (A): 43.92200 81.20200 zmin,zma (A): -60.25700 -9.719001 x,y,z range (A): 43.52600 37.28001 50.53800 scale (grids/A): 2.113261 object centre (A): 48.88400 62.56200 -34.98800 number of atom coordinates read : 2037 total number of charged atoms : 1912 net assigned charge : 6.500010 assigned positive charge : 308.6971 centred at (gu) : 91.83675 89.11488 87.14266 assigned negative charge : -302.1972 centred at (gu) : 92.35548 89.25270 87.16683 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73881 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17639 grid for indexing accessible points = 1.400000 m= 30522 mr = 52290 m= 5898 mr = 22912 m= 520 mr = 3830 m= 11 mr = 235 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 31565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15182 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) : 0.7044204 object centre at (A) : 48.88400 62.56200 -34.98800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0124517E-02 2.5112262E-02 midg,1,midg; midg,igrid,midg 2.9107304E-02 7.2676651E-03 1,midg,midg; igrid,midg,midg 3.8675319E-02 1.3876196E-02 gauss-seidel spectral radius is 0.9988214 estimated iterations to convergence 231 setup time was (sec) 0.9200000 now iterating at: 06:13:29 rms-change max change #iterations 4.490281 198.7297 at 10iterations 2.226712 76.86236 at 20iterations 1.098374 36.37582 at 30iterations 0.5414777 16.90130 at 40iterations 0.2700440 8.874676 at 50iterations 0.1333029 4.209208 at 60iterations 6.6183731E-02 2.029255 at 70iterations 3.2888662E-02 0.9471283 at 80iterations 1.6419737E-02 0.5375729 at 90iterations 8.2643665E-03 0.2366320 at 100iterations 4.2299507E-03 0.1271667 at 110iterations 2.2464520E-03 6.6955566E-02 at 120iterations finished qdiffx linear iterations at : 06:13:38 total time elapsed so far: 10.31000 # loops : 120 mean,max change (kT/e) : 2.2464520E-03 6.6955566E-02 energy calculations done at 10.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.48000 DelPhi exited at 06:13:39 10.481u 0.442s 0:11.35 96.2% 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 06:13:39 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 = 2037 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: 3.169892 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): 27.12100 70.64700 ymin,ymax (A): 43.92200 81.20200 zmin,zma (A): -60.25700 -9.719001 x,y,z range (A): 43.52600 37.28001 50.53800 scale (grids/A): 3.169892 object centre (A): 48.88400 62.56200 -34.98800 number of atom coordinates read : 2037 total number of charged atoms : 1912 net assigned charge : 6.500010 assigned positive charge : 308.6971 centred at (gu) : 92.75511 88.67240 85.71400 assigned negative charge : -302.1972 centred at (gu) : 93.53336 88.87909 85.75019 start vw surface at 0.1000000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 169877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17639 grid for indexing accessible points = 1.400000 m= 94452 mr = 125604 m= 39080 mr = 78353 m= 10980 mr = 31700 m= 2033 mr = 8321 m= 204 mr = 1353 m= 6 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.910000 number of dielectric boundary points 71200 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 15296 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) : 2.113261 object centre at (A) : 48.88400 62.56200 -34.98800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2810189 6.8298243E-02 midg,1,midg; midg,igrid,midg 0.2363358 5.1007248E-02 1,midg,midg; igrid,midg,midg 0.3227215 0.2268068 gauss-seidel spectral radius is 0.9992934 estimated iterations to convergence 297 setup time was (sec) 2.250000 now iterating at: 06:13:42 rms-change max change #iterations 10.10632 381.7991 at 10iterations 6.017645 161.8091 at 20iterations 3.569551 66.10577 at 30iterations 2.110158 40.50313 at 40iterations 1.244421 26.84642 at 50iterations 0.7315690 13.67833 at 60iterations 0.4303799 7.588380 at 70iterations 0.2530416 4.778610 at 80iterations 0.1483641 2.724651 at 90iterations 8.7107688E-02 1.515782 at 100iterations 5.1073883E-02 0.9630966 at 110iterations 3.0148998E-02 0.6599386 at 120iterations 1.7988803E-02 0.3275375 at 130iterations 1.0872054E-02 0.1992264 at 140iterations 6.7922696E-03 0.1149826 at 150iterations 4.4327793E-03 8.0078125E-02 at 160iterations 3.0857273E-03 5.5168152E-02 at 170iterations 2.2960494E-03 3.9623260E-02 at 180iterations finished qdiffx linear iterations at : 06:13:58 total time elapsed so far: 17.92000 # loops : 180 mean,max change (kT/e) : 2.2960494E-03 3.9623260E-02 energy calculations done at 17.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.09000 DelPhi exited at 06:13:58 18.098u 0.463s 0:18.88 98.2% 0+0k 0+0io 0pf+0w