Tue Oct 11 03:39:59 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 03:39:59 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6067837 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): -12.06600 36.72600 ymin,ymax (A): -27.01500 21.55300 zmin,zma (A): -13.30900 45.36100 x,y,z range (A): 48.79200 48.56800 58.67000 scale (grids/A): 0.6067837 object centre (A): 12.33000 -2.731000 16.02600 number of atom coordinates read : 2838 total number of charged atoms : 2683 net assigned charge : 0.1620197 assigned positive charge : 429.1526 centred at (gu) : 90.22422 90.60724 92.31225 assigned negative charge : -428.9912 centred at (gu) : 89.97350 90.47373 92.18247 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6759 nv = 96 ne = 84 npr = 58399 no. pairs analyzed = 58399 no. exposed pairs = 3350 no. arc points = 23128 no. surface atoms = 1134 nbur = 1704 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 328 mr = 3803 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3400000 number of dielectric boundary points 3251 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2394 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8527 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9335486E-09 1.0572539E-08 midg,1,midg; midg,igrid,midg -5.9402905E-09 7.3137194E-09 1,midg,midg; igrid,midg,midg -1.2228107E-08 1.2528165E-08 gauss-seidel spectral radius is 0.9859533 estimated iterations to convergence 69 setup time was (sec) 0.5600000 now iterating at: 03:40:00 rms-change max change #iterations 0.1208717 18.45300 at 10iterations 1.0613675E-02 1.721966 at 20iterations 9.3327102E-04 0.1373119 at 30iterations 8.2684150E-05 1.1327744E-02 at 40iterations 7.7800069E-06 1.1043549E-03 at 50iterations finished qdiffx linear iterations at : 03:40:03 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 7.7800069E-06 1.1043549E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 03:40:03 3.372u 0.154s 0:03.86 91.1% 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 03:40:03 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.820351 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): -12.06600 36.72600 ymin,ymax (A): -27.01500 21.55300 zmin,zma (A): -13.30900 45.36100 x,y,z range (A): 48.79200 48.56800 58.67000 scale (grids/A): 1.820351 object centre (A): 12.33000 -2.731000 16.02600 number of atom coordinates read : 2838 total number of charged atoms : 2683 net assigned charge : 0.1620197 assigned positive charge : 429.1526 centred at (gu) : 90.67225 91.82117 96.93616 assigned negative charge : -428.9912 centred at (gu) : 89.92023 91.42100 96.54728 start vw surface at 0.2300000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 73759 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23128 grid for indexing accessible points = 1.400000 m= 26108 mr = 51953 m= 3421 mr = 19387 m= 155 mr = 2092 m= 0 mr = 50 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1190 time to turn everything in is 0.5900000 number of dielectric boundary points 29961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 212 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 20992 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) : 0.6067837 object centre at (A) : 12.33000 -2.731000 16.02600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2882118E-02 3.9167209E-03 midg,1,midg; midg,igrid,midg -9.2616174E-03 1.1907909E-02 1,midg,midg; igrid,midg,midg -8.4773367E-03 4.1788924E-02 gauss-seidel spectral radius is 0.9985257 estimated iterations to convergence 207 setup time was (sec) 0.8800000 now iterating at: 03:40:04 rms-change max change #iterations 4.102797 182.9990 at 10iterations 1.866841 73.54425 at 20iterations 0.8496050 32.51793 at 30iterations 0.3871644 12.65489 at 40iterations 0.1768762 5.857513 at 50iterations 8.0700919E-02 3.073414 at 60iterations 3.6702782E-02 1.168317 at 70iterations 1.6743707E-02 0.5518036 at 80iterations 7.6251230E-03 0.2325745 at 90iterations 3.4682681E-03 0.1133499 at 100iterations 1.5827632E-03 5.3775787E-02 at 110iterations 7.2209438E-04 2.1598816E-02 at 120iterations finished qdiffx linear iterations at : 03:40:10 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 7.2209438E-04 2.1598816E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.120000 DelPhi exited at 03:40:11 7.122u 0.206s 0:07.71 94.9% 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 03:40:11 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.730527 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): -12.06600 36.72600 ymin,ymax (A): -27.01500 21.55300 zmin,zma (A): -13.30900 45.36100 x,y,z range (A): 48.79200 48.56800 58.67000 scale (grids/A): 2.730527 object centre (A): 12.33000 -2.731000 16.02600 number of atom coordinates read : 2838 total number of charged atoms : 2683 net assigned charge : 0.1620197 assigned positive charge : 429.1526 centred at (gu) : 91.00819 92.73181 100.4042 assigned negative charge : -428.9912 centred at (gu) : 89.88033 92.13142 99.82099 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 170925 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23128 grid for indexing accessible points = 1.400000 m= 86605 mr = 125809 m= 28576 mr = 71375 m= 5957 mr = 23019 m= 714 mr = 4560 m= 37 mr = 468 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 3894 time to turn everything in is 1.250000 number of dielectric boundary points 67576 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 21459 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) : 1.820351 object centre at (A) : 12.33000 -2.731000 16.02600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.350288 0.2456594 midg,1,midg; midg,igrid,midg -0.1218558 0.1565132 1,midg,midg; igrid,midg,midg -5.3554296E-02 0.4175267 gauss-seidel spectral radius is 0.9992265 estimated iterations to convergence 284 setup time was (sec) 1.530000 now iterating at: 03:40:13 rms-change max change #iterations 9.706893 291.8512 at 10iterations 5.579372 118.4504 at 20iterations 3.193150 76.20934 at 30iterations 1.820978 38.06219 at 40iterations 1.037698 19.42630 at 50iterations 0.5918779 10.72867 at 60iterations 0.3368243 6.057682 at 70iterations 0.1918664 3.585037 at 80iterations 0.1087586 2.055477 at 90iterations 6.1843034E-02 1.168921 at 100iterations 3.5171039E-02 0.6594391 at 110iterations 2.0000158E-02 0.3785286 at 120iterations 1.1352961E-02 0.2216606 at 130iterations 6.4755767E-03 0.1263479 at 140iterations 3.6651469E-03 6.7130089E-02 at 150iterations 2.0859377E-03 3.8860321E-02 at 160iterations 1.1889567E-03 2.1881104E-02 at 170iterations 6.7883357E-04 1.2634277E-02 at 180iterations finished qdiffx linear iterations at : 03:40:22 total time elapsed so far: 11.07000 # loops : 180 mean,max change (kT/e) : 6.7883357E-04 1.2634277E-02 energy calculations done at 11.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.24000 DelPhi exited at 03:40:23 11.243u 0.237s 0:11.82 97.0% 0+0k 0+0io 0pf+0w