Mon Oct 10 16:32:41 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 Mon Oct 10 2011 at 16:32:41 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2309 !!! WARNING: ASL 34 has a net charge of -0.1000 !!! WARNING: GLM 40 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6357483 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): 29.76600 85.76300 ymin,ymax (A): 28.84800 76.46900 zmin,zma (A): -27.94600 21.48900 x,y,z range (A): 55.99700 47.62100 49.43500 scale (grids/A): 0.6357483 object centre (A): 57.76450 52.65850 -3.228499 number of atom coordinates read : 2309 total number of charged atoms : 2228 net assigned charge : -1.194001 assigned positive charge : 342.9901 centred at (gu) : 89.09277 91.05112 90.11189 assigned negative charge : -344.1849 centred at (gu) : 89.24096 91.07420 90.10358 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6232 nv = 96 ne = 84 npr = 46061 no. pairs analyzed = 46061 no. exposed pairs = 3154 no. arc points = 22350 no. surface atoms = 1063 nbur = 1246 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 396 mr = 3095 m= 4 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3494 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2188 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7679 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3475637E-09 -8.9451613E-10 midg,1,midg; midg,igrid,midg 3.6481507E-10 -4.7269548E-09 1,midg,midg; igrid,midg,midg 1.4394439E-08 -1.2715041E-08 gauss-seidel spectral radius is 0.9871655 estimated iterations to convergence 72 setup time was (sec) 0.3800000 now iterating at: 16:32:41 rms-change max change #iterations 0.1314177 26.01502 at 10iterations 1.2691079E-02 2.576508 at 20iterations 1.2193307E-03 0.1768475 at 30iterations 1.2000190E-04 1.7904282E-02 at 40iterations 1.1888485E-05 2.0489693E-03 at 50iterations finished qdiffx linear iterations at : 16:32:44 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.1888485E-05 2.0489693E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 16:32:45 3.398u 0.159s 0:04.08 86.7% 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 16:32:45 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2309 !!! WARNING: ASL 34 has a net charge of -0.1000 !!! WARNING: GLM 40 has a net charge of -0.0940 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: 1.907245 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): 29.76600 85.76300 ymin,ymax (A): 28.84800 76.46900 zmin,zma (A): -27.94600 21.48900 x,y,z range (A): 55.99700 47.62100 49.43500 scale (grids/A): 1.907245 object centre (A): 57.76450 52.65850 -3.228499 number of atom coordinates read : 2309 total number of charged atoms : 2228 net assigned charge : -1.194001 assigned positive charge : 342.9901 centred at (gu) : 87.27785 93.15327 90.33526 assigned negative charge : -344.1849 centred at (gu) : 87.72282 93.22256 90.31059 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66276 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22350 grid for indexing accessible points = 1.400000 m= 23913 mr = 43258 m= 4558 mr = 16834 m= 342 mr = 2761 m= 2 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 32112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 17560 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) : 0.6357483 object centre at (A) : 57.76450 52.65850 -3.228499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9693460E-02 -8.1102195E-04 midg,1,midg; midg,igrid,midg -3.3429073E-04 -3.5339966E-02 1,midg,midg; igrid,midg,midg 7.9467781E-02 -6.2200818E-03 gauss-seidel spectral radius is 0.9986237 estimated iterations to convergence 214 setup time was (sec) 0.5500000 now iterating at: 16:32:46 rms-change max change #iterations 3.997193 193.6934 at 10iterations 1.854503 75.07008 at 20iterations 0.8647199 33.78902 at 30iterations 0.4035974 13.44168 at 40iterations 0.1886099 6.244567 at 50iterations 8.7841898E-02 3.275302 at 60iterations 4.0945020E-02 1.432024 at 70iterations 1.9147683E-02 0.6519306 at 80iterations 8.9229345E-03 0.3396339 at 90iterations 4.1677020E-03 0.1525278 at 100iterations 1.9402343E-03 6.5534592E-02 at 110iterations 9.1055810E-04 2.9622078E-02 at 120iterations finished qdiffx linear iterations at : 16:32:53 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 9.1055810E-04 2.9622078E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 16:32:54 7.768u 0.205s 0:08.55 93.0% 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 16:32:54 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2309 !!! WARNING: ASL 34 has a net charge of -0.1000 !!! WARNING: GLM 40 has a net charge of -0.0940 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: 2.860868 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): 29.76600 85.76300 ymin,ymax (A): 28.84800 76.46900 zmin,zma (A): -27.94600 21.48900 x,y,z range (A): 55.99700 47.62100 49.43500 scale (grids/A): 2.860868 object centre (A): 57.76450 52.65850 -3.228499 number of atom coordinates read : 2309 total number of charged atoms : 2228 net assigned charge : -1.194001 assigned positive charge : 342.9901 centred at (gu) : 85.91653 94.72964 90.50277 assigned negative charge : -344.1849 centred at (gu) : 86.58418 94.83375 90.46595 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 153186 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22350 grid for indexing accessible points = 1.400000 m= 74930 mr = 105907 m= 29434 mr = 59058 m= 8401 mr = 22918 m= 1372 mr = 6223 m= 79 mr = 870 m= 0 mr = 36 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8900000 number of dielectric boundary points 72390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 17824 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) : 1.907245 object centre at (A) : 57.76450 52.65850 -3.228499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3711203 5.7608023E-02 midg,1,midg; midg,igrid,midg 4.8740925E-03 -0.4245354 1,midg,midg; igrid,midg,midg 1.277083 -5.9785757E-02 gauss-seidel spectral radius is 0.9992603 estimated iterations to convergence 290 setup time was (sec) 1.120000 now iterating at: 16:32:55 rms-change max change #iterations 9.540391 370.1710 at 10iterations 5.640793 181.6173 at 20iterations 3.298097 74.46735 at 30iterations 1.930343 43.54128 at 40iterations 1.119926 22.00219 at 50iterations 0.6509793 13.67811 at 60iterations 0.3765265 8.109911 at 70iterations 0.2176334 4.011041 at 80iterations 0.1258540 2.647773 at 90iterations 7.2410628E-02 1.445796 at 100iterations 4.1567843E-02 0.8091164 at 110iterations 2.4001095E-02 0.4860058 at 120iterations 1.3787135E-02 0.2658215 at 130iterations 7.9111513E-03 0.1576233 at 140iterations 4.5521175E-03 8.6843491E-02 at 150iterations 2.6182788E-03 4.8683167E-02 at 160iterations 1.5050841E-03 2.8302670E-02 at 170iterations 8.6474261E-04 1.6061783E-02 at 180iterations finished qdiffx linear iterations at : 16:33:06 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 8.6474261E-04 1.6061783E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 16:33:07 12.543u 0.200s 0:13.34 95.5% 0+0k 0+0io 0pf+0w