Tue Oct 11 01:06:40 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 01:06:40 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2590 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6400000 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): -2.416000 53.20900 ymin,ymax (A): 5.672000 58.38900 zmin,zma (A): 7.214000 50.23600 x,y,z range (A): 55.62500 52.71700 43.02200 scale (grids/A): 0.6400000 object centre (A): 25.39650 32.03050 28.72500 number of atom coordinates read : 2590 total number of charged atoms : 2448 net assigned charge : 4.000012 assigned positive charge : 391.4369 centred at (gu) : 89.19664 89.17039 90.27670 assigned negative charge : -387.4373 centred at (gu) : 89.32154 89.12846 90.46189 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7090 nv = 96 ne = 84 npr = 52862 no. pairs analyzed = 52862 no. exposed pairs = 3075 no. arc points = 21352 no. surface atoms = 1050 nbur = 1540 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 374 mr = 4020 m= 0 mr = 41 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2000000 number of dielectric boundary points 3403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2076 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8472 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5387781E-08 -1.7183616E-08 midg,1,midg; midg,igrid,midg 1.0475191E-09 8.9724637E-09 1,midg,midg; igrid,midg,midg 2.3983464E-08 -7.4257320E-09 gauss-seidel spectral radius is 0.9873485 estimated iterations to convergence 73 setup time was (sec) 0.4000000 now iterating at: 01:06:41 rms-change max change #iterations 0.1506250 18.27145 at 10iterations 1.6140357E-02 2.261719 at 20iterations 2.2965902E-03 0.4124298 at 30iterations 5.3558609E-04 0.1129341 at 40iterations 1.5331458E-04 3.2321930E-02 at 50iterations finished qdiffx linear iterations at : 01:06:44 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.5331458E-04 3.2321930E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 01:06:44 3.355u 0.147s 0:03.84 90.8% 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 01:06:44 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2590 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.920000 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): -2.416000 53.20900 ymin,ymax (A): 5.672000 58.38900 zmin,zma (A): 7.214000 50.23600 x,y,z range (A): 55.62500 52.71700 43.02200 scale (grids/A): 1.920000 object centre (A): 25.39650 32.03050 28.72500 number of atom coordinates read : 2590 total number of charged atoms : 2448 net assigned charge : 4.000012 assigned positive charge : 391.4369 centred at (gu) : 87.58909 87.51073 90.82951 assigned negative charge : -387.4373 centred at (gu) : 87.96447 87.38538 91.38551 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76780 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21352 grid for indexing accessible points = 1.400000 m= 27726 mr = 54089 m= 4376 mr = 20794 m= 244 mr = 2733 m= 6 mr = 95 m= 0 mr = 1 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 590 time to turn everything in is 0.3700000 number of dielectric boundary points 31420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19258 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) : 0.6400000 object centre at (A) : 25.39650 32.03050 28.72500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3013109E-02 3.3639695E-03 midg,1,midg; midg,igrid,midg -6.6250446E-03 1.0705728E-02 1,midg,midg; igrid,midg,midg 2.8111003E-02 -2.1416692E-02 gauss-seidel spectral radius is 0.9986498 estimated iterations to convergence 216 setup time was (sec) 0.5800000 now iterating at: 01:06:45 rms-change max change #iterations 4.342300 169.2290 at 10iterations 2.034781 70.24564 at 20iterations 0.9593941 31.79812 at 30iterations 0.4490626 15.72916 at 40iterations 0.2115481 7.493515 at 50iterations 9.9720135E-02 3.026855 at 60iterations 4.7115132E-02 1.428894 at 70iterations 2.2336306E-02 0.7336349 at 80iterations 1.0760421E-02 0.3308372 at 90iterations 5.2516507E-03 0.1752281 at 100iterations 2.6313877E-03 9.3074799E-02 at 110iterations 1.4010323E-03 5.3989410E-02 at 120iterations finished qdiffx linear iterations at : 01:06:52 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 1.4010323E-03 5.3989410E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 01:06:53 7.671u 0.187s 0:08.50 92.3% 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 01:06:53 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2590 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.880000 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): -2.416000 53.20900 ymin,ymax (A): 5.672000 58.38900 zmin,zma (A): 7.214000 50.23600 x,y,z range (A): 55.62500 52.71700 43.02200 scale (grids/A): 2.880000 object centre (A): 25.39650 32.03050 28.72500 number of atom coordinates read : 2590 total number of charged atoms : 2448 net assigned charge : 4.000012 assigned positive charge : 391.4369 centred at (gu) : 86.38354 86.26596 91.24415 assigned negative charge : -387.4373 centred at (gu) : 86.94662 86.07803 92.07822 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 177787 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21352 grid for indexing accessible points = 1.400000 m= 90733 mr = 131117 m= 32474 mr = 75049 m= 7685 mr = 26246 m= 1060 mr = 5885 m= 61 mr = 681 m= 3 mr = 29 m= 0 mr = 1 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 2162 time to turn everything in is 0.9600000 number of dielectric boundary points 70795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 19579 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) : 1.920000 object centre at (A) : 25.39650 32.03050 28.72500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3188797 0.1001430 midg,1,midg; midg,igrid,midg 0.2167138 0.1584013 1,midg,midg; igrid,midg,midg 0.2927584 -0.1704315 gauss-seidel spectral radius is 0.9992567 estimated iterations to convergence 289 setup time was (sec) 1.200000 now iterating at: 01:06:54 rms-change max change #iterations 10.04699 427.9673 at 10iterations 5.797021 117.5496 at 20iterations 3.346393 61.41374 at 30iterations 1.924105 39.48171 at 40iterations 1.110480 21.52327 at 50iterations 0.6363016 11.35378 at 60iterations 0.3663136 7.037769 at 70iterations 0.2103393 3.848888 at 80iterations 0.1208062 2.306908 at 90iterations 6.9483571E-02 1.232407 at 100iterations 3.9966073E-02 0.7681236 at 110iterations 2.3051387E-02 0.4676514 at 120iterations 1.3370699E-02 0.2448034 at 130iterations 7.8615453E-03 0.1559753 at 140iterations 4.7209864E-03 9.4432831E-02 at 150iterations 2.9116159E-03 6.4434052E-02 at 160iterations 1.8760988E-03 4.2510986E-02 at 170iterations 1.2923573E-03 3.0574799E-02 at 180iterations finished qdiffx linear iterations at : 01:07:05 total time elapsed so far: 12.25000 # loops : 180 mean,max change (kT/e) : 1.2923573E-03 3.0574799E-02 energy calculations done at 12.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 01:07:06 12.382u 0.196s 0:12.91 97.3% 0+0k 0+0io 0pf+0w