Tue Nov 22 14:22:51 PST 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 Nov 22 2011 at 14:22:55 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5906655 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): -35.20100 9.815000 ymin,ymax (A): 1.235000 41.22700 zmin,zma (A): -1.562000 58.70900 x,y,z range (A): 45.01600 39.99200 60.27100 scale (grids/A): 0.5906655 object centre (A): -12.69300 21.23100 28.57350 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 1.000005 assigned positive charge : 291.4660 centred at (gu) : 90.51552 89.54119 89.48382 assigned negative charge : -290.4663 centred at (gu) : 90.45215 89.63659 89.47047 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4584 nv = 96 ne = 84 npr = 40361 no. pairs analyzed = 40361 no. exposed pairs = 2432 no. arc points = 16947 no. surface atoms = 823 nbur = 1143 mkacc time = 7.0000008E-02 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= 219 mr = 2525 m= 0 mr = 15 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2263 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1731 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 5642 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9219814E-11 5.0817162E-10 midg,1,midg; midg,igrid,midg 2.4719540E-09 -1.4931166E-09 1,midg,midg; igrid,midg,midg -8.8444652E-10 1.7824543E-09 gauss-seidel spectral radius is 0.9851167 estimated iterations to convergence 67 setup time was (sec) 0.3700000 now iterating at: 14:22:59 rms-change max change #iterations 9.1035090E-02 18.60789 at 10iterations 7.3326775E-03 1.332563 at 20iterations 5.8988418E-04 0.1050631 at 30iterations 4.7310645E-05 8.3293915E-03 at 40iterations 3.8573230E-06 7.3242188E-04 at 50iterations finished qdiffx linear iterations at : 14:23:09 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 3.8573230E-06 7.3242188E-04 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 14:23:10 3.761u 0.225s 0:15.39 25.8% 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 Nov 22 2011 at 14:23:12 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.771996 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): -35.20100 9.815000 ymin,ymax (A): 1.235000 41.22700 zmin,zma (A): -1.562000 58.70900 x,y,z range (A): 45.01600 39.99200 60.27100 scale (grids/A): 1.771996 object centre (A): -12.69300 21.23100 28.57350 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 1.000005 assigned positive charge : 291.4660 centred at (gu) : 91.54633 88.62345 88.45141 assigned negative charge : -290.4663 centred at (gu) : 91.35678 88.90978 88.41146 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 49288 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16947 grid for indexing accessible points = 1.400000 m= 17585 mr = 33601 m= 2328 mr = 13209 m= 108 mr = 1500 m= 0 mr = 43 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 163 time to turn everything in is 0.2700000 number of dielectric boundary points 20956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 216 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 14307 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) : 0.5906655 object centre at (A) : -12.69300 21.23100 28.57350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6351921E-02 2.0070301E-02 midg,1,midg; midg,igrid,midg -1.3752317E-03 -6.7134262E-03 1,midg,midg; igrid,midg,midg -2.7858519E-03 -6.2478408E-03 gauss-seidel spectral radius is 0.9983461 estimated iterations to convergence 195 setup time was (sec) 0.5400000 now iterating at: 14:23:17 rms-change max change #iterations 3.135269 158.9915 at 10iterations 1.349358 57.03621 at 20iterations 0.5898224 23.02115 at 30iterations 0.2551825 10.60789 at 40iterations 0.1104096 4.205235 at 50iterations 4.7959078E-02 1.905884 at 60iterations 2.0766102E-02 0.7908332 at 70iterations 9.0244459E-03 0.3341370 at 80iterations 3.9144531E-03 0.1454697 at 90iterations 1.6915416E-03 6.4230919E-02 at 100iterations 7.3505152E-04 2.8460264E-02 at 110iterations 3.2025983E-04 1.2668610E-02 at 120iterations finished qdiffx linear iterations at : 14:23:42 total time elapsed so far: 8.910000 # loops : 120 mean,max change (kT/e) : 3.2025983E-04 1.2668610E-02 energy calculations done at 8.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.050000 DelPhi exited at 14:23:44 9.048u 0.271s 0:31.61 29.4% 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 Tue Nov 22 2011 at 14:23:46 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.657995 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): -35.20100 9.815000 ymin,ymax (A): 1.235000 41.22700 zmin,zma (A): -1.562000 58.70900 x,y,z range (A): 45.01600 39.99200 60.27100 scale (grids/A): 2.657995 object centre (A): -12.69300 21.23100 28.57350 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 1.000005 assigned positive charge : 291.4660 centred at (gu) : 92.31966 87.93525 87.67718 assigned negative charge : -290.4663 centred at (gu) : 92.03524 88.36484 87.61719 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 113983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16947 grid for indexing accessible points = 1.400000 m= 57065 mr = 81430 m= 20180 mr = 46996 m= 4157 mr = 16711 m= 488 mr = 3233 m= 19 mr = 343 m= 0 mr = 8 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 536 time to turn everything in is 0.6700000 number of dielectric boundary points 47171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 14668 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) : 1.771996 object centre at (A) : -12.69300 21.23100 28.57350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2527951 0.1333476 midg,1,midg; midg,igrid,midg -4.7045920E-02 -9.9357560E-02 1,midg,midg; igrid,midg,midg -5.4825712E-02 -0.1260731 gauss-seidel spectral radius is 0.9991556 estimated iterations to convergence 272 setup time was (sec) 0.9400000 now iterating at: 14:23:52 rms-change max change #iterations 7.581078 246.5075 at 10iterations 4.209451 115.4398 at 20iterations 2.339984 61.69182 at 30iterations 1.293844 31.68491 at 40iterations 0.7138602 16.72318 at 50iterations 0.3951605 8.606674 at 60iterations 0.2177336 5.155766 at 70iterations 0.1203833 2.609536 at 80iterations 6.6211514E-02 1.597931 at 90iterations 3.6596447E-02 0.8973556 at 100iterations 2.0094804E-02 0.4622550 at 110iterations 1.1098268E-02 0.2564087 at 120iterations 6.1502582E-03 0.1309986 at 130iterations 3.3884514E-03 7.2414756E-02 at 140iterations 1.8638063E-03 4.3160558E-02 at 150iterations 1.0305154E-03 2.2378564E-02 at 160iterations 5.6867377E-04 1.1896133E-02 at 170iterations 3.1366225E-04 7.3280334E-03 at 180iterations finished qdiffx linear iterations at : 14:24:29 total time elapsed so far: 13.29000 # loops : 180 mean,max change (kT/e) : 3.1366225E-04 7.3280334E-03 energy calculations done at 13.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.42000 DelPhi exited at 14:24:30 13.423u 0.277s 0:44.69 30.6% 0+0k 0+0io 0pf+0w