Sun Oct 9 08:27:18 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 Sun Oct 9 2011 at 08:27:18 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 = 5811 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: 0.4803022 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): 3.918000 78.03800 ymin,ymax (A): 21.94200 84.07100 zmin,zma (A): 6.700000 72.11500 x,y,z range (A): 74.12000 62.12900 65.41500 scale (grids/A): 0.4803022 object centre (A): 40.97800 53.00650 39.40750 number of atom coordinates read : 5811 total number of charged atoms : 5645 net assigned charge : 1.500050 assigned positive charge : 874.3862 centred at (gu) : 89.48242 88.92169 89.14946 assigned negative charge : -872.8937 centred at (gu) : 89.32310 88.91631 89.06606 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8274 nv = 96 ne = 84 npr = 117075 no. pairs analyzed = 117075 no. exposed pairs = 7288 no. arc points = 50471 no. surface atoms = 2442 nbur = 3369 mkacc time = 0.2000000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 270 mr = 4181 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4354 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4756 ## 820 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 11292 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.7453245E-11 5.7009144E-11 midg,1,midg; midg,igrid,midg 3.0512767E-12 8.0907017E-12 1,midg,midg; igrid,midg,midg -1.4306047E-10 1.1317612E-10 gauss-seidel spectral radius is 0.9779175 estimated iterations to convergence 56 setup time was (sec) 0.5500000 now iterating at: 08:27:19 rms-change max change #iterations 5.4346967E-02 10.02929 at 10iterations 2.6653954E-03 0.4211426 at 20iterations 2.4388723E-04 5.5084229E-02 at 30iterations 5.2414129E-05 1.2544632E-02 at 40iterations 1.3842778E-05 3.0899048E-03 at 50iterations finished qdiffx linear iterations at : 08:27:22 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 1.3842778E-05 3.0899048E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 08:27:22 3.556u 0.183s 0:04.02 92.7% 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 Sun Oct 9 2011 at 08:27:22 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 = 5811 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.440907 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): 3.918000 78.03800 ymin,ymax (A): 21.94200 84.07100 zmin,zma (A): 6.700000 72.11500 x,y,z range (A): 74.12000 62.12900 65.41500 scale (grids/A): 1.440907 object centre (A): 40.97800 53.00650 39.40750 number of atom coordinates read : 5811 total number of charged atoms : 5645 net assigned charge : 1.500050 assigned positive charge : 874.3862 centred at (gu) : 88.44569 86.76307 87.44660 assigned negative charge : -872.8937 centred at (gu) : 87.96876 86.74860 87.19799 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 94899 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50471 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 25070 mr = 64589 m= 1660 mr = 15742 m= 19 mr = 578 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 651 time to turn everything in is 0.4600000 number of dielectric boundary points 40737 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 817 ## 16 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 41308 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) : 0.4803022 object centre at (A) : 40.97800 53.00650 39.40750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7623051E-03 4.0388475E-03 midg,1,midg; midg,igrid,midg -9.8905968E-04 -2.7241530E-03 1,midg,midg; igrid,midg,midg -5.5607944E-03 2.1548688E-02 gauss-seidel spectral radius is 0.9979297 estimated iterations to convergence 175 setup time was (sec) 0.6700000 now iterating at: 08:27:23 rms-change max change #iterations 3.659184 150.4396 at 10iterations 1.433586 52.67654 at 20iterations 0.5649882 17.96182 at 30iterations 0.2224011 7.390846 at 40iterations 8.7218732E-02 2.717751 at 50iterations 3.4565706E-02 1.174835 at 60iterations 1.3632297E-02 0.5137687 at 70iterations 5.3987405E-03 0.1874385 at 80iterations 2.1372065E-03 6.6977501E-02 at 90iterations 8.5660187E-04 2.8173447E-02 at 100iterations 3.4952222E-04 1.2947083E-02 at 110iterations 1.5027855E-04 5.7325363E-03 at 120iterations finished qdiffx linear iterations at : 08:27:30 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 1.5027855E-04 5.7325363E-03 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 08:27:31 8.005u 0.224s 0:08.55 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 Sun Oct 9 2011 at 08:27:31 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 = 5811 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: 2.161360 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): 3.918000 78.03800 ymin,ymax (A): 21.94200 84.07100 zmin,zma (A): 6.700000 72.11500 x,y,z range (A): 74.12000 62.12900 65.41500 scale (grids/A): 2.161360 object centre (A): 40.97800 53.00650 39.40750 number of atom coordinates read : 5811 total number of charged atoms : 5645 net assigned charge : 1.500050 assigned positive charge : 874.3862 centred at (gu) : 87.66811 85.14422 86.16925 assigned negative charge : -872.8937 centred at (gu) : 86.95313 85.12277 85.79681 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 222140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50471 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 93520 mr = 160095 m= 20042 mr = 70922 m= 2063 mr = 13647 m= 69 mr = 1109 m= 0 mr = 21 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 2277 time to turn everything in is 1.100000 number of dielectric boundary points 92040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 44909 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) : 1.440907 object centre at (A) : 40.97800 53.00650 39.40750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1719058 2.1502769E-02 midg,1,midg; midg,igrid,midg -1.8440895E-02 -3.1856429E-02 1,midg,midg; igrid,midg,midg 4.9218632E-02 0.3646463 gauss-seidel spectral radius is 0.9991347 estimated iterations to convergence 269 setup time was (sec) 1.350000 now iterating at: 08:27:32 rms-change max change #iterations 10.42700 282.4130 at 10iterations 5.960709 153.2125 at 20iterations 3.381244 72.33990 at 30iterations 1.905439 38.55283 at 40iterations 1.070462 24.07048 at 50iterations 0.5994763 13.91445 at 60iterations 0.3343388 6.859378 at 70iterations 0.1862330 3.740754 at 80iterations 0.1035210 2.146717 at 90iterations 5.7512235E-02 1.042528 at 100iterations 3.1784058E-02 0.6954403 at 110iterations 1.7610541E-02 0.3565159 at 120iterations 9.7253239E-03 0.1849327 at 130iterations 5.3859991E-03 0.1100373 at 140iterations 2.9845173E-03 5.8753967E-02 at 150iterations 1.6481943E-03 3.1679153E-02 at 160iterations 9.1207714E-04 1.7822266E-02 at 170iterations 5.0626294E-04 9.6721649E-03 at 180iterations finished qdiffx linear iterations at : 08:27:44 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 5.0626294E-04 9.6721649E-03 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 08:27:44 12.892u 0.205s 0:13.41 97.6% 0+0k 0+0io 0pf+0w