Sat Oct 8 11:33:56 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 11:33:56 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 = 4464 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: 0.5793139 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): -25.54500 34.23700 ymin,ymax (A): 37.75400 99.20600 zmin,zma (A): 30.34500 89.72200 x,y,z range (A): 59.78201 61.45200 59.37700 scale (grids/A): 0.5793139 object centre (A): 4.346002 68.48000 60.03350 number of atom coordinates read : 4464 total number of charged atoms : 4304 net assigned charge : -2.499960 assigned positive charge : 670.1241 centred at (gu) : 90.45189 87.77539 88.54283 assigned negative charge : -672.6273 centred at (gu) : 90.36732 87.86235 88.64056 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 9564 nv = 96 ne = 84 npr = 95058 no. pairs analyzed = 95058 no. exposed pairs = 4887 no. arc points = 33253 no. surface atoms = 1663 nbur = 2801 mkacc time = 0.1600000 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 = 1.484000 m= 440 mr = 5677 m= 0 mr = 28 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 66 time to turn everything in is 0.3100000 number of dielectric boundary points 4299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3515 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 12586 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5066763E-09 -2.7375224E-09 midg,1,midg; midg,igrid,midg 3.6544852E-09 -2.0805482E-09 1,midg,midg; igrid,midg,midg -3.0746690E-09 2.2807052E-09 gauss-seidel spectral radius is 0.9847236 estimated iterations to convergence 66 setup time was (sec) 0.5100000 now iterating at: 11:33:57 rms-change max change #iterations 0.1223646 16.07802 at 10iterations 9.7858720E-03 1.629202 at 20iterations 9.1083924E-04 0.1054230 at 30iterations 1.4076926E-04 1.9058228E-02 at 40iterations 4.3243203E-05 6.0662031E-03 at 50iterations finished qdiffx linear iterations at : 11:34:00 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 4.3243203E-05 6.0662031E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 11:34:00 3.621u 0.189s 0:04.16 91.3% 0+0k 0+0io 6pf+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 11:34:00 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 = 4464 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: 1.737942 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): -25.54500 34.23700 ymin,ymax (A): 37.75400 99.20600 zmin,zma (A): 30.34500 89.72200 x,y,z range (A): 59.78201 61.45200 59.37700 scale (grids/A): 1.737942 object centre (A): 4.346002 68.48000 60.03350 number of atom coordinates read : 4464 total number of charged atoms : 4304 net assigned charge : -2.499960 assigned positive charge : 670.1241 centred at (gu) : 91.35443 83.32501 85.62720 assigned negative charge : -672.6273 centred at (gu) : 91.10150 83.58678 85.92106 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 106133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33253 grid for indexing accessible points = 1.400000 m= 36176 mr = 77707 m= 4727 mr = 26919 m= 206 mr = 2965 m= 0 mr = 53 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 4983 time to turn everything in is 0.5100000 number of dielectric boundary points 39598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 324 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 33368 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) : 0.5793139 object centre at (A) : 4.346002 68.48000 60.03350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1764258E-03 -2.7664907E-02 midg,1,midg; midg,igrid,midg 4.8590556E-02 6.3281278E-03 1,midg,midg; igrid,midg,midg -7.6059923E-03 3.6801860E-02 gauss-seidel spectral radius is 0.9985214 estimated iterations to convergence 206 setup time was (sec) 0.7400000 now iterating at: 11:34:01 rms-change max change #iterations 4.815904 184.6812 at 10iterations 2.189070 69.67784 at 20iterations 0.9956250 30.79863 at 30iterations 0.4532717 12.79970 at 40iterations 0.2066804 5.438927 at 50iterations 9.4010279E-02 2.486305 at 60iterations 4.2876795E-02 1.129762 at 70iterations 1.9535720E-02 0.5058308 at 80iterations 8.8920584E-03 0.2450664 at 90iterations 4.0697190E-03 0.1179130 at 100iterations 1.8592017E-03 5.2455902E-02 at 110iterations 8.5917400E-04 2.5266647E-02 at 120iterations finished qdiffx linear iterations at : 11:34:09 total time elapsed so far: 8.210000 # loops : 120 mean,max change (kT/e) : 8.5917400E-04 2.5266647E-02 energy calculations done at 8.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.340000 DelPhi exited at 11:34:09 8.345u 0.219s 0:08.97 95.3% 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 11:34:09 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 = 4464 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: 2.606913 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): -25.54500 34.23700 ymin,ymax (A): 37.75400 99.20600 zmin,zma (A): 30.34500 89.72200 x,y,z range (A): 59.78201 61.45200 59.37700 scale (grids/A): 2.606913 object centre (A): 4.346002 68.48000 60.03350 number of atom coordinates read : 4464 total number of charged atoms : 4304 net assigned charge : -2.499960 assigned positive charge : 670.1241 centred at (gu) : 92.03129 79.98714 83.44055 assigned negative charge : -672.6273 centred at (gu) : 91.65199 80.38007 83.88149 start vw surface at 0.1200000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 247096 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33253 grid for indexing accessible points = 1.400000 m= 122513 mr = 188505 m= 39101 mr = 101607 m= 8204 mr = 31559 m= 913 mr = 6232 m= 27 mr = 602 m= 0 mr = 2 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 16435 time to turn everything in is 1.300000 number of dielectric boundary points 89347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 34425 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) : 1.737942 object centre at (A) : 4.346002 68.48000 60.03350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1478965 -0.3187052 midg,1,midg; midg,igrid,midg 0.6736175 0.1578071 1,midg,midg; igrid,midg,midg -0.1892429 0.3868263 gauss-seidel spectral radius is 0.9992539 estimated iterations to convergence 289 setup time was (sec) 1.560000 now iterating at: 11:34:11 rms-change max change #iterations 11.72399 291.4709 at 10iterations 6.843465 158.2454 at 20iterations 3.971471 66.78134 at 30iterations 2.302622 41.61197 at 40iterations 1.326943 21.85329 at 50iterations 0.7667010 12.81217 at 60iterations 0.4426703 7.547910 at 70iterations 0.2543484 4.036277 at 80iterations 0.1463846 2.454793 at 90iterations 8.4065691E-02 1.378487 at 100iterations 4.8338469E-02 0.8116493 at 110iterations 2.7768362E-02 0.4295686 at 120iterations 1.5942760E-02 0.2611382 at 130iterations 9.1929482E-03 0.1431518 at 140iterations 5.2765249E-03 8.0478668E-02 at 150iterations 3.0415182E-03 4.7737122E-02 at 160iterations 1.7580671E-03 2.8026581E-02 at 170iterations 1.0224193E-03 1.8710613E-02 at 180iterations finished qdiffx linear iterations at : 11:34:23 total time elapsed so far: 13.70000 # loops : 180 mean,max change (kT/e) : 1.0224193E-03 1.8710613E-02 energy calculations done at 13.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.82000 DelPhi exited at 11:34:24 13.821u 0.234s 0:14.54 96.6% 0+0k 0+0io 0pf+0w