Mon Oct 10 11:05:00 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 Mon Oct 10 2011 at 11:05:00 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 = 5349 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5046854 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): -0.2660000 70.27299 ymin,ymax (A): -39.97500 28.67000 zmin,zma (A): -29.37300 35.18300 x,y,z range (A): 70.53899 68.64500 64.55600 scale (grids/A): 0.5046854 object centre (A): 35.00350 -5.652501 2.905000 number of atom coordinates read : 5349 total number of charged atoms : 5195 net assigned charge : 13.00002 assigned positive charge : 843.2050 centred at (gu) : 88.52984 90.70050 91.02888 assigned negative charge : -830.2127 centred at (gu) : 88.56779 90.64845 91.09731 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8711 nv = 96 ne = 84 npr = 105298 no. pairs analyzed = 105298 no. exposed pairs = 6620 no. arc points = 44722 no. surface atoms = 2211 nbur = 3138 mkacc time = 0.2200000 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 = 1.680000 m= 325 mr = 4762 m= 0 mr = 9 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.4900000 number of dielectric boundary points 4265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4410 ## 695 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 11672 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2709186E-10 -2.9361784E-11 midg,1,midg; midg,igrid,midg 1.6064594E-11 3.1342987E-10 1,midg,midg; igrid,midg,midg 3.3678155E-10 3.6294169E-11 gauss-seidel spectral radius is 0.9799606 estimated iterations to convergence 58 setup time was (sec) 0.7200000 now iterating at: 11:05:01 rms-change max change #iterations 6.7501709E-02 9.643047 at 10iterations 3.8913698E-03 0.5897141 at 20iterations 6.3692121E-04 0.1060724 at 30iterations 3.1362276E-04 4.8830509E-02 at 40iterations 1.6548739E-04 2.5511265E-02 at 50iterations finished qdiffx linear iterations at : 11:05:04 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.6548739E-04 2.5511265E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 11:05:04 3.539u 0.209s 0:04.07 91.6% 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 Mon Oct 10 2011 at 11:05:04 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 = 5349 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.514056 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): -0.2660000 70.27299 ymin,ymax (A): -39.97500 28.67000 zmin,zma (A): -29.37300 35.18300 x,y,z range (A): 70.53899 68.64500 64.55600 scale (grids/A): 1.514056 object centre (A): 35.00350 -5.652501 2.905000 number of atom coordinates read : 5349 total number of charged atoms : 5195 net assigned charge : 13.00002 assigned positive charge : 843.2050 centred at (gu) : 85.58766 92.09969 93.08494 assigned negative charge : -830.2127 centred at (gu) : 85.70349 91.94521 93.29204 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 99731 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44722 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 29305 mr = 70569 m= 2372 mr = 19912 m= 38 mr = 960 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1918 time to turn everything in is 0.6700000 number of dielectric boundary points 40005 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 675 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 38809 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) : 0.5046854 object centre at (A) : 35.00350 -5.652501 2.905000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9279904E-03 6.4492819E-04 midg,1,midg; midg,igrid,midg -3.8299237E-03 1.8445795E-02 1,midg,midg; igrid,midg,midg 2.6146157E-02 -1.6558463E-02 gauss-seidel spectral radius is 0.9981055 estimated iterations to convergence 183 setup time was (sec) 0.9700000 now iterating at: 11:05:05 rms-change max change #iterations 3.997937 152.1967 at 10iterations 1.639949 51.64742 at 20iterations 0.6703892 20.90232 at 30iterations 0.2748379 8.171970 at 40iterations 0.1127760 3.437550 at 50iterations 4.6261184E-02 1.545631 at 60iterations 1.9008895E-02 0.6120853 at 70iterations 7.8769894E-03 0.2502327 at 80iterations 3.3226602E-03 0.1138039 at 90iterations 1.5126675E-03 4.9448013E-02 at 100iterations 7.9284160E-04 2.9093742E-02 at 110iterations 5.1244767E-04 1.8955231E-02 at 120iterations finished qdiffx linear iterations at : 11:05:12 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 5.1244767E-04 1.8955231E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 11:05:13 7.778u 0.218s 0:08.26 96.6% 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 Mon Oct 10 2011 at 11:05:13 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 = 5349 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.271084 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): -0.2660000 70.27299 ymin,ymax (A): -39.97500 28.67000 zmin,zma (A): -29.37300 35.18300 x,y,z range (A): 70.53899 68.64500 64.55600 scale (grids/A): 2.271084 object centre (A): 35.00350 -5.652501 2.905000 number of atom coordinates read : 5349 total number of charged atoms : 5195 net assigned charge : 13.00002 assigned positive charge : 843.2050 centred at (gu) : 83.38092 93.14920 94.62687 assigned negative charge : -830.2127 centred at (gu) : 83.55540 92.91785 94.93822 start vw surface at 0.1800000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 233207 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44722 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 105878 mr = 173373 m= 26108 mr = 83902 m= 3393 mr = 18953 m= 151 mr = 2067 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 6314 time to turn everything in is 1.660000 number of dielectric boundary points 90413 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 84 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 41420 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) : 1.514056 object centre at (A) : 35.00350 -5.652501 2.905000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1125461E-02 -5.9801448E-02 midg,1,midg; midg,igrid,midg -0.1689739 0.3938163 1,midg,midg; igrid,midg,midg 0.2674283 -0.5394711 gauss-seidel spectral radius is 0.9991639 estimated iterations to convergence 273 setup time was (sec) 2.000000 now iterating at: 11:05:15 rms-change max change #iterations 10.93621 297.4956 at 10iterations 6.294713 154.7397 at 20iterations 3.575813 80.52914 at 30iterations 2.024536 53.78389 at 40iterations 1.140634 27.39205 at 50iterations 0.6402981 13.92311 at 60iterations 0.3583537 6.942759 at 70iterations 0.2003814 3.888311 at 80iterations 0.1118931 2.254354 at 90iterations 6.2362008E-02 1.182034 at 100iterations 3.4728847E-02 0.6434655 at 110iterations 1.9337045E-02 0.3499660 at 120iterations 1.0748255E-02 0.2252007 at 130iterations 5.9792064E-03 0.1081619 at 140iterations 3.3239836E-03 5.8250904E-02 at 150iterations 1.8477370E-03 3.5762787E-02 at 160iterations 1.0280418E-03 1.9237518E-02 at 170iterations 5.7063886E-04 1.0825634E-02 at 180iterations finished qdiffx linear iterations at : 11:05:26 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 5.7063886E-04 1.0825634E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 11:05:26 13.109u 0.260s 0:13.65 97.8% 0+0k 0+0io 0pf+0w