Mon Oct 10 17:03:05 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 17:03:05 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 = 2765 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: 0.5526577 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): 17.47000 64.88600 ymin,ymax (A): -9.516000 41.58700 zmin,zma (A): -1.976000 62.44000 x,y,z range (A): 47.41600 51.10300 64.41600 scale (grids/A): 0.5526577 object centre (A): 41.17800 16.03550 30.23200 number of atom coordinates read : 2765 total number of charged atoms : 2626 net assigned charge : 6.000022 assigned positive charge : 406.4386 centred at (gu) : 90.47396 89.35845 89.24505 assigned negative charge : -400.4397 centred at (gu) : 90.45263 89.21124 89.27933 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5550 nv = 96 ne = 84 npr = 55621 no. pairs analyzed = 55621 no. exposed pairs = 3711 no. arc points = 25582 no. surface atoms = 1239 nbur = 1526 mkacc time = 0.1400000 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 = 1.540000 m= 229 mr = 2764 m= 0 mr = 10 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3005 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2636 ## 310 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7181 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0144270E-10 1.9078238E-10 midg,1,midg; midg,igrid,midg -7.7759349E-10 1.3641266E-09 1,midg,midg; igrid,midg,midg 2.9178568E-10 7.3106710E-10 gauss-seidel spectral radius is 0.9831021 estimated iterations to convergence 63 setup time was (sec) 0.6100000 now iterating at: 17:03:06 rms-change max change #iterations 7.1901627E-02 11.90962 at 10iterations 4.9489518E-03 0.9417038 at 20iterations 3.6542470E-04 6.5246582E-02 at 30iterations 3.3799963E-05 5.4000616E-03 at 40iterations 4.1849557E-06 5.4645538E-04 at 50iterations finished qdiffx linear iterations at : 17:03:10 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 4.1849557E-06 5.4645538E-04 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.520000 DelPhi exited at 17:03:11 4.526u 0.384s 0:05.35 91.5% 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 Mon Oct 10 2011 at 17:03:11 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 = 2765 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: 1.657973 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): 17.47000 64.88600 ymin,ymax (A): -9.516000 41.58700 zmin,zma (A): -1.976000 62.44000 x,y,z range (A): 47.41600 51.10300 64.41600 scale (grids/A): 1.657973 object centre (A): 41.17800 16.03550 30.23200 number of atom coordinates read : 2765 total number of charged atoms : 2626 net assigned charge : 6.000022 assigned positive charge : 406.4386 centred at (gu) : 91.42113 88.07488 87.73470 assigned negative charge : -400.4397 centred at (gu) : 91.35793 87.63366 87.83801 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 61179 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25582 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18678 mr = 40664 m= 2050 mr = 12433 m= 52 mr = 977 m= 0 mr = 6 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 82 time to turn everything in is 0.5000000 number of dielectric boundary points 27879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 273 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 20163 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) : 0.5526577 object centre at (A) : 41.17800 16.03550 30.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3447355E-02 1.7130280E-02 midg,1,midg; midg,igrid,midg -7.0039923E-03 9.5059285E-03 1,midg,midg; igrid,midg,midg 6.1042694E-04 1.8409227E-03 gauss-seidel spectral radius is 0.9982214 estimated iterations to convergence 188 setup time was (sec) 0.7900000 now iterating at: 17:03:12 rms-change max change #iterations 3.267334 151.6483 at 10iterations 1.365022 57.16330 at 20iterations 0.5749261 23.11467 at 30iterations 0.2426509 9.968770 at 40iterations 0.1016665 3.836003 at 50iterations 4.2826936E-02 1.727192 at 60iterations 1.8026514E-02 0.6985836 at 70iterations 7.5637079E-03 0.2892876 at 80iterations 3.1834813E-03 0.1181974 at 90iterations 1.3421258E-03 6.0570717E-02 at 100iterations 5.6637364E-04 2.0916462E-02 at 110iterations 2.3817593E-04 8.5209608E-03 at 120iterations finished qdiffx linear iterations at : 17:03:21 total time elapsed so far: 10.10000 # loops : 120 mean,max change (kT/e) : 2.3817593E-04 8.5209608E-03 energy calculations done at 10.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.26000 DelPhi exited at 17:03:22 10.268u 0.474s 0:11.05 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 Mon Oct 10 2011 at 17:03:22 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 = 2765 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: 2.486960 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): 17.47000 64.88600 ymin,ymax (A): -9.516000 41.58700 zmin,zma (A): -1.976000 62.44000 x,y,z range (A): 47.41600 51.10300 64.41600 scale (grids/A): 2.486960 object centre (A): 41.17800 16.03550 30.23200 number of atom coordinates read : 2765 total number of charged atoms : 2626 net assigned charge : 6.000022 assigned positive charge : 406.4386 centred at (gu) : 92.13145 87.11221 86.60196 assigned negative charge : -400.4397 centred at (gu) : 92.03682 86.45047 86.75688 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 142130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25582 grid for indexing accessible points = 1.400000 m= 64701 mr = 99926 m= 18430 mr = 50202 m= 3179 mr = 13480 m= 210 mr = 2037 m= 3 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 261 time to turn everything in is 1.240000 number of dielectric boundary points 62930 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 20980 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) : 1.657973 object centre at (A) : 41.17800 16.03550 30.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2998243 0.4471643 midg,1,midg; midg,igrid,midg -5.6464531E-02 0.1522139 1,midg,midg; igrid,midg,midg 1.9231983E-02 1.1371631E-02 gauss-seidel spectral radius is 0.9991500 estimated iterations to convergence 271 setup time was (sec) 1.550000 now iterating at: 17:03:24 rms-change max change #iterations 8.465024 293.1255 at 10iterations 4.823164 176.6136 at 20iterations 2.728564 79.16148 at 30iterations 1.523573 41.82742 at 40iterations 0.8524855 20.71095 at 50iterations 0.4734792 9.968811 at 60iterations 0.2629893 6.393616 at 70iterations 0.1458540 3.303061 at 80iterations 8.0749318E-02 1.963429 at 90iterations 4.4609793E-02 1.003197 at 100iterations 2.4648942E-02 0.5248985 at 110iterations 1.3617670E-02 0.2945683 at 120iterations 7.5105396E-03 0.1687965 at 130iterations 4.1470677E-03 9.6765280E-02 at 140iterations 2.2862705E-03 4.8591614E-02 at 150iterations 1.2610853E-03 2.6845932E-02 at 160iterations 6.9582666E-04 1.4421701E-02 at 170iterations 3.8327553E-04 8.4800720E-03 at 180iterations finished qdiffx linear iterations at : 17:03:39 total time elapsed so far: 16.92000 # loops : 180 mean,max change (kT/e) : 3.8327553E-04 8.4800720E-03 energy calculations done at 16.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.09000 DelPhi exited at 17:03:40 17.090u 0.492s 0:17.90 98.2% 0+0k 0+0io 0pf+0w