Tue Oct 11 08:40:51 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 08:40:51 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3219 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 0.5882645 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): 0.8189999 49.12500 ymin,ymax (A): -7.879000 49.42500 zmin,zma (A): 0.8010000 61.31800 x,y,z range (A): 48.30600 57.30400 60.51700 scale (grids/A): 0.5882645 object centre (A): 24.97200 20.77300 31.05950 number of atom coordinates read : 3219 total number of charged atoms : 3048 net assigned charge : -9.9990666E-02 assigned positive charge : 479.2349 centred at (gu) : 89.52180 89.28860 90.74363 assigned negative charge : -479.3360 centred at (gu) : 89.40200 89.24669 90.66578 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7293 nv = 96 ne = 84 npr = 66040 no. pairs analyzed = 66040 no. exposed pairs = 3845 no. arc points = 25674 no. surface atoms = 1304 nbur = 1915 mkacc time = 0.1700000 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 = 1.456000 m= 334 mr = 4184 m= 0 mr = 27 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.3600000 number of dielectric boundary points 3416 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2679 ## 262 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9271 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0638697E-09 2.8401752E-09 midg,1,midg; midg,igrid,midg -1.5664395E-09 1.0838053E-09 1,midg,midg; igrid,midg,midg -4.2444777E-09 3.2675120E-09 gauss-seidel spectral radius is 0.9850959 estimated iterations to convergence 67 setup time was (sec) 0.6400000 now iterating at: 08:40:52 rms-change max change #iterations 0.1096110 15.21476 at 10iterations 9.7676851E-03 1.275069 at 20iterations 1.4145145E-03 0.2334023 at 30iterations 4.2949498E-04 7.7653885E-02 at 40iterations 1.4789858E-04 2.6950836E-02 at 50iterations finished qdiffx linear iterations at : 08:40:57 total time elapsed so far: 4.730000 # loops : 50 mean,max change (kT/e) : 1.4789858E-04 2.6950836E-02 energy calculations done at 4.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.890000 DelPhi exited at 08:40:57 4.899u 0.394s 0:05.73 92.1% 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 08:40:57 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3219 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.764793 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): 0.8189999 49.12500 ymin,ymax (A): -7.879000 49.42500 zmin,zma (A): 0.8010000 61.31800 x,y,z range (A): 48.30600 57.30400 60.51700 scale (grids/A): 1.764793 object centre (A): 24.97200 20.77300 31.05950 number of atom coordinates read : 3219 total number of charged atoms : 3048 net assigned charge : -9.9990666E-02 assigned positive charge : 479.2349 centred at (gu) : 88.56478 87.86494 92.23029 assigned negative charge : -479.3360 centred at (gu) : 88.20561 87.73972 91.99699 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80230 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25674 grid for indexing accessible points = 1.400000 m= 29259 mr = 57287 m= 4017 mr = 22254 m= 156 mr = 2548 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 3819 time to turn everything in is 0.6600000 number of dielectric boundary points 31550 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 23727 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) : 0.5882645 object centre at (A) : 24.97200 20.77300 31.05950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7502336E-02 4.2954641E-03 midg,1,midg; midg,igrid,midg -1.5728658E-02 7.2129276E-03 1,midg,midg; igrid,midg,midg -1.1461764E-02 1.3919332E-02 gauss-seidel spectral radius is 0.9984744 estimated iterations to convergence 203 setup time was (sec) 0.9700000 now iterating at: 08:40:59 rms-change max change #iterations 4.109032 174.3319 at 10iterations 1.843921 70.03320 at 20iterations 0.8291354 25.36161 at 30iterations 0.3725735 12.78368 at 40iterations 0.1680607 5.232382 at 50iterations 7.5700462E-02 2.678126 at 60iterations 3.4158498E-02 1.192123 at 70iterations 1.5507141E-02 0.4702778 at 80iterations 7.1402257E-03 0.2277851 at 90iterations 3.3629758E-03 0.1239014 at 100iterations 1.6780408E-03 5.8961868E-02 at 110iterations 9.0892258E-04 3.4290314E-02 at 120iterations finished qdiffx linear iterations at : 08:41:10 total time elapsed so far: 12.32000 # loops : 120 mean,max change (kT/e) : 9.0892258E-04 3.4290314E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.49000 DelPhi exited at 08:41:11 12.497u 0.449s 0:13.34 96.9% 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 08:41:11 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3219 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.647190 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): 0.8189999 49.12500 ymin,ymax (A): -7.879000 49.42500 zmin,zma (A): 0.8010000 61.31800 x,y,z range (A): 48.30600 57.30400 60.51700 scale (grids/A): 2.647190 object centre (A): 24.97200 20.77300 31.05950 number of atom coordinates read : 3219 total number of charged atoms : 3048 net assigned charge : -9.9990666E-02 assigned positive charge : 479.2349 centred at (gu) : 87.84694 86.79728 93.34531 assigned negative charge : -479.3360 centred at (gu) : 87.30833 86.60947 92.99539 start vw surface at 0.1400000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 185846 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25674 grid for indexing accessible points = 1.400000 m= 96155 mr = 138653 m= 33471 mr = 80052 m= 7042 mr = 27455 m= 634 mr = 5409 m= 14 mr = 405 m= 0 mr = 1 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 12744 time to turn everything in is 1.790000 number of dielectric boundary points 71187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 24378 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) : 1.764793 object centre at (A) : 24.97200 20.77300 31.05950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4279898 -0.2484898 midg,1,midg; midg,igrid,midg -0.3196271 7.9231285E-02 1,midg,midg; igrid,midg,midg -0.1368480 0.1521466 gauss-seidel spectral radius is 0.9992211 estimated iterations to convergence 283 setup time was (sec) 2.190000 now iterating at: 08:41:13 rms-change max change #iterations 9.999290 264.0189 at 10iterations 5.768157 135.4466 at 20iterations 3.312358 90.14655 at 30iterations 1.890535 40.01158 at 40iterations 1.079901 20.66803 at 50iterations 0.6153577 12.34890 at 60iterations 0.3511122 6.859780 at 70iterations 0.1997577 3.651112 at 80iterations 0.1134694 2.140882 at 90iterations 6.4314447E-02 1.180401 at 100iterations 3.6612961E-02 0.6897888 at 110iterations 2.0843122E-02 0.3833699 at 120iterations 1.1901032E-02 0.2111807 at 130iterations 6.8253134E-03 0.1164799 at 140iterations 3.9602872E-03 7.3822021E-02 at 150iterations 2.3499883E-03 4.4044495E-02 at 160iterations 1.4456640E-03 3.3987999E-02 at 170iterations 9.3627075E-04 2.0149231E-02 at 180iterations finished qdiffx linear iterations at : 08:41:32 total time elapsed so far: 20.60000 # loops : 180 mean,max change (kT/e) : 9.3627075E-04 2.0149231E-02 energy calculations done at 20.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.77000 DelPhi exited at 08:41:32 20.778u 0.477s 0:21.85 97.2% 0+0k 0+0io 0pf+0w