Sat Oct 8 22:09:26 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 Sat Oct 8 2011 at 22:09:26 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 = 3388 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5567806 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): -47.24800 7.237000 ymin,ymax (A): 176.3350 239.6040 zmin,zma (A): 78.16100 142.1000 x,y,z range (A): 54.48500 63.26900 63.93900 scale (grids/A): 0.5567806 object centre (A): -20.00550 207.9695 110.1305 number of atom coordinates read : 3388 total number of charged atoms : 3244 net assigned charge : 13.50003 assigned positive charge : 501.3665 centred at (gu) : 89.84173 90.16528 90.87794 assigned negative charge : -487.8683 centred at (gu) : 89.73716 90.13533 91.02509 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7013 nv = 96 ne = 84 npr = 65604 no. pairs analyzed = 65604 no. exposed pairs = 4679 no. arc points = 32975 no. surface atoms = 1544 nbur = 1844 mkacc time = 0.1900000 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 = 1.568000 m= 335 mr = 3440 m= 0 mr = 8 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.4400000 number of dielectric boundary points 3900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3344 ## 391 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 9146 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3121796E-09 -4.2968204E-10 midg,1,midg; midg,igrid,midg 9.2949148E-10 1.6793963E-09 1,midg,midg; igrid,midg,midg 1.4717712E-10 2.3193403E-09 gauss-seidel spectral radius is 0.9834086 estimated iterations to convergence 64 setup time was (sec) 0.7200000 now iterating at: 22:09:27 rms-change max change #iterations 8.3675027E-02 15.03824 at 10iterations 5.9709945E-03 0.8974657 at 20iterations 4.4137501E-04 6.7587376E-02 at 30iterations 3.8361206E-05 5.6018829E-03 at 40iterations 5.5297678E-06 8.5115433E-04 at 50iterations finished qdiffx linear iterations at : 22:09:30 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 5.5297678E-06 8.5115433E-04 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 22:09:31 4.094u 0.161s 0:04.53 93.8% 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 Sat Oct 8 2011 at 22:09:31 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 = 3388 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.670342 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): -47.24800 7.237000 ymin,ymax (A): 176.3350 239.6040 zmin,zma (A): 78.16100 142.1000 x,y,z range (A): 54.48500 63.26900 63.93900 scale (grids/A): 1.670342 object centre (A): -20.00550 207.9695 110.1305 number of atom coordinates read : 3388 total number of charged atoms : 3244 net assigned charge : 13.50003 assigned positive charge : 501.3665 centred at (gu) : 89.52407 90.49493 92.63307 assigned negative charge : -487.8683 centred at (gu) : 89.21091 90.40599 93.07497 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 77330 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32975 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24416 mr = 50736 m= 2860 mr = 16445 m= 100 mr = 1466 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1845 time to turn everything in is 0.7100000 number of dielectric boundary points 36041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 375 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 24977 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) : 0.5567806 object centre at (A) : -20.00550 207.9695 110.1305 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4876426E-03 -1.0183403E-02 midg,1,midg; midg,igrid,midg 2.2499122E-02 2.9272757E-02 1,midg,midg; igrid,midg,midg -9.7862154E-04 1.7783144E-02 gauss-seidel spectral radius is 0.9983321 estimated iterations to convergence 194 setup time was (sec) 1.050000 now iterating at: 22:09:32 rms-change max change #iterations 3.712544 161.7495 at 10iterations 1.593906 58.87985 at 20iterations 0.6858073 21.71027 at 30iterations 0.2962861 9.985180 at 40iterations 0.1273288 4.625300 at 50iterations 5.5188295E-02 1.715483 at 60iterations 2.3793256E-02 0.8770761 at 70iterations 1.0259384E-02 0.3375130 at 80iterations 4.4439440E-03 0.1448898 at 90iterations 1.9221473E-03 6.5231323E-02 at 100iterations 8.3088741E-04 2.7193069E-02 at 110iterations 3.6015495E-04 1.2302399E-02 at 120iterations finished qdiffx linear iterations at : 22:09:40 total time elapsed so far: 8.770000 # loops : 120 mean,max change (kT/e) : 3.6015495E-04 1.2302399E-02 energy calculations done at 8.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.990000 DelPhi exited at 22:09:40 8.997u 0.188s 0:09.51 96.4% 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 Sat Oct 8 2011 at 22:09:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3388 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.505513 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): -47.24800 7.237000 ymin,ymax (A): 176.3350 239.6040 zmin,zma (A): 78.16100 142.1000 x,y,z range (A): 54.48500 63.26900 63.93900 scale (grids/A): 2.505513 object centre (A): -20.00550 207.9695 110.1305 number of atom coordinates read : 3388 total number of charged atoms : 3244 net assigned charge : 13.50003 assigned positive charge : 501.3665 centred at (gu) : 89.28609 90.74205 93.94950 assigned negative charge : -487.8683 centred at (gu) : 88.81641 90.60896 94.61250 start vw surface at 0.2200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 179408 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32975 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 82353 mr = 124581 m= 25175 mr = 64103 m= 4563 mr = 18718 m= 425 mr = 3019 m= 8 mr = 195 m= 0 mr = 0 time to grow re-entrant surface = 0.9900001 no. cavity mid-points inaccessible to solvent = 6271 time to turn everything in is 1.710000 number of dielectric boundary points 81316 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 25938 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) : 1.670342 object centre at (A) : -20.00550 207.9695 110.1305 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2135656 -0.1622277 midg,1,midg; midg,igrid,midg 0.3117144 0.5101624 1,midg,midg; igrid,midg,midg -6.2335726E-02 0.1801306 gauss-seidel spectral radius is 0.9992042 estimated iterations to convergence 280 setup time was (sec) 2.080000 now iterating at: 22:09:43 rms-change max change #iterations 9.460510 306.1537 at 10iterations 5.480971 143.3990 at 20iterations 3.142256 69.04437 at 30iterations 1.796305 36.44773 at 40iterations 1.022752 23.08992 at 50iterations 0.5811628 11.94110 at 60iterations 0.3288763 7.338541 at 70iterations 0.1862558 4.072350 at 80iterations 0.1052002 2.054567 at 90iterations 5.9281342E-02 1.104454 at 100iterations 3.3473507E-02 0.6689177 at 110iterations 1.8862117E-02 0.3853092 at 120iterations 1.0614392E-02 0.1894327 at 130iterations 5.9887823E-03 0.1098690 at 140iterations 3.3663416E-03 6.7909241E-02 at 150iterations 1.8982217E-03 3.4486771E-02 at 160iterations 1.0656482E-03 1.9780159E-02 at 170iterations 6.0105073E-04 1.2144089E-02 at 180iterations finished qdiffx linear iterations at : 22:09:55 total time elapsed so far: 14.28000 # loops : 180 mean,max change (kT/e) : 6.0105073E-04 1.2144089E-02 energy calculations done at 14.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.51000 DelPhi exited at 22:09:55 14.512u 0.209s 0:14.99 98.1% 0+0k 0+0io 0pf+0w