Sat Oct 15 13:04:30 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 15 2011 at 13:04:30 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 = 2474 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6295760 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): -19.90800 34.09200 ymin,ymax (A): -25.85500 30.69100 zmin,zma (A): -10.61900 39.34100 x,y,z range (A): 54.00000 56.54600 49.96000 scale (grids/A): 0.6295760 object centre (A): 7.092002 2.418000 14.36100 number of atom coordinates read : 2474 total number of charged atoms : 2336 net assigned charge : 8.500010 assigned positive charge : 367.4230 centred at (gu) : 90.76351 90.24457 90.50198 assigned negative charge : -358.9238 centred at (gu) : 90.91140 90.38605 90.31001 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6527 nv = 96 ne = 84 npr = 49925 no. pairs analyzed = 49925 no. exposed pairs = 3112 no. arc points = 21900 no. surface atoms = 1061 nbur = 1413 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 3429 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3000000 number of dielectric boundary points 3418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2235 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7955 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8907852E-09 2.7204823E-08 midg,1,midg; midg,igrid,midg 1.9406496E-08 -2.5684317E-09 1,midg,midg; igrid,midg,midg 1.7782583E-08 -3.5846752E-09 gauss-seidel spectral radius is 0.9869216 estimated iterations to convergence 72 setup time was (sec) 0.6100000 now iterating at: 13:04:31 rms-change max change #iterations 0.1253757 19.56951 at 10iterations 1.1833763E-02 1.808052 at 20iterations 1.1302721E-03 0.1683526 at 30iterations 1.2013946E-04 1.7645836E-02 at 40iterations 1.7349315E-05 3.1089783E-03 at 50iterations finished qdiffx linear iterations at : 13:04:36 total time elapsed so far: 5.000000 # loops : 50 mean,max change (kT/e) : 1.7349315E-05 3.1089783E-03 energy calculations done at 5.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.170000 DelPhi exited at 13:04:36 5.171u 0.479s 0:06.03 93.5% 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 15 2011 at 13:04:37 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 = 2474 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.888728 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): -19.90800 34.09200 ymin,ymax (A): -25.85500 30.69100 zmin,zma (A): -10.61900 39.34100 x,y,z range (A): 54.00000 56.54600 49.96000 scale (grids/A): 1.888728 object centre (A): 7.092002 2.418000 14.36100 number of atom coordinates read : 2474 total number of charged atoms : 2336 net assigned charge : 8.500010 assigned positive charge : 367.4230 centred at (gu) : 92.28998 90.73296 91.50560 assigned negative charge : -358.9238 centred at (gu) : 92.73422 91.15813 90.92984 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70792 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21900 grid for indexing accessible points = 1.400000 m= 23746 mr = 48210 m= 3306 mr = 16571 m= 205 mr = 1828 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 676 time to turn everything in is 0.6000000 number of dielectric boundary points 31373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 18333 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) : 0.6295760 object centre at (A) : 7.092002 2.418000 14.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0548976E-03 4.1136652E-02 midg,1,midg; midg,igrid,midg 2.3616111E-02 -3.8304657E-02 1,midg,midg; igrid,midg,midg 3.0888958E-02 4.8236097E-03 gauss-seidel spectral radius is 0.9985948 estimated iterations to convergence 211 setup time was (sec) 0.9500000 now iterating at: 13:04:38 rms-change max change #iterations 3.961475 165.1099 at 10iterations 1.827440 63.70183 at 20iterations 0.8511117 31.22302 at 30iterations 0.3927259 14.50805 at 40iterations 0.1821223 7.191637 at 50iterations 8.4217593E-02 2.811462 at 60iterations 3.9011773E-02 1.290226 at 70iterations 1.8087495E-02 0.5830553 at 80iterations 8.3669154E-03 0.2626598 at 90iterations 3.8736826E-03 0.1244955 at 100iterations 1.8026910E-03 5.3255081E-02 at 110iterations 8.3573995E-04 2.8036118E-02 at 120iterations finished qdiffx linear iterations at : 13:04:49 total time elapsed so far: 12.26000 # loops : 120 mean,max change (kT/e) : 8.3573995E-04 2.8036118E-02 energy calculations done at 12.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.44000 DelPhi exited at 13:04:50 12.447u 0.536s 0:13.35 97.1% 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 15 2011 at 13:04:50 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 = 2474 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.833092 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): -19.90800 34.09200 ymin,ymax (A): -25.85500 30.69100 zmin,zma (A): -10.61900 39.34100 x,y,z range (A): 54.00000 56.54600 49.96000 scale (grids/A): 2.833092 object centre (A): 7.092002 2.418000 14.36100 number of atom coordinates read : 2474 total number of charged atoms : 2336 net assigned charge : 8.500010 assigned positive charge : 367.4230 centred at (gu) : 93.43488 91.09930 92.25829 assigned negative charge : -358.9238 centred at (gu) : 94.10116 91.73704 91.39471 start vw surface at 0.1300000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 163839 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21900 grid for indexing accessible points = 1.400000 m= 79007 mr = 117500 m= 25863 mr = 63103 m= 5882 mr = 19627 m= 842 mr = 4055 m= 44 mr = 515 m= 0 mr = 13 time to grow re-entrant surface = 0.9599999 no. cavity mid-points inaccessible to solvent = 2155 time to turn everything in is 1.610000 number of dielectric boundary points 70664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 18688 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) : 1.888728 object centre at (A) : 7.092002 2.418000 14.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6131773E-02 0.4629715 midg,1,midg; midg,igrid,midg 0.3281927 -0.5283024 1,midg,midg; igrid,midg,midg 0.4066157 5.2654613E-02 gauss-seidel spectral radius is 0.9992494 estimated iterations to convergence 288 setup time was (sec) 2.060000 now iterating at: 13:04:52 rms-change max change #iterations 9.493188 340.9530 at 10iterations 5.570547 127.7422 at 20iterations 3.223094 69.63691 at 30iterations 1.870895 39.27359 at 40iterations 1.078193 21.22736 at 50iterations 0.6212106 11.65780 at 60iterations 0.3578101 6.960221 at 70iterations 0.2050120 4.023586 at 80iterations 0.1177548 2.462255 at 90iterations 6.7610823E-02 1.399289 at 100iterations 3.8776062E-02 0.7156718 at 110iterations 2.2236610E-02 0.4165192 at 120iterations 1.2737755E-02 0.2534348 at 130iterations 7.2779190E-03 0.1402781 at 140iterations 4.1715000E-03 7.7365875E-02 at 150iterations 2.3933654E-03 4.6563148E-02 at 160iterations 1.3656418E-03 2.4160385E-02 at 170iterations 7.8220130E-04 1.3624191E-02 at 180iterations finished qdiffx linear iterations at : 13:05:11 total time elapsed so far: 21.01000 # loops : 180 mean,max change (kT/e) : 7.8220130E-04 1.3624191E-02 energy calculations done at 21.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.17000 DelPhi exited at 13:05:12 21.179u 0.560s 0:22.06 98.5% 0+0k 0+0io 0pf+0w