Sun Oct 9 15:41:21 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 Sun Oct 9 2011 at 15:41:21 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5659 !!! WARNING: HIR 201 has a net charge of 0.5140 !!! WARNING: HIR 748 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5053230 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): 67.29600 137.7460 ymin,ymax (A): -6.234000 56.98200 zmin,zma (A): -3.312000 65.75400 x,y,z range (A): 70.44999 63.21600 69.06599 scale (grids/A): 0.5053230 object centre (A): 102.5210 25.37400 31.22100 number of atom coordinates read : 5659 total number of charged atoms : 5488 net assigned charge : -3.471964 assigned positive charge : 868.0021 centred at (gu) : 89.94557 90.83993 90.24436 assigned negative charge : -871.4819 centred at (gu) : 90.00533 90.76737 90.34357 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8814 nv = 96 ne = 84 npr = 117164 no. pairs analyzed = 117164 no. exposed pairs = 6427 no. arc points = 44364 no. surface atoms = 2156 nbur = 3503 mkacc time = 0.2000000 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 = 1.708000 m= 292 mr = 4830 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.3800000 number of dielectric boundary points 4262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4294 ## 629 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 12030 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9364195E-10 -3.1318351E-10 midg,1,midg; midg,igrid,midg -1.7938954E-10 1.7799065E-10 1,midg,midg; igrid,midg,midg 1.1125685E-10 -1.8885854E-10 gauss-seidel spectral radius is 0.9800228 estimated iterations to convergence 58 setup time was (sec) 0.5700000 now iterating at: 15:41:22 rms-change max change #iterations 7.1260922E-02 9.476028 at 10iterations 4.6097720E-03 0.6476593 at 20iterations 7.0625363E-04 0.1069889 at 30iterations 1.9184084E-04 2.7379990E-02 at 40iterations 5.6403300E-05 7.2898865E-03 at 50iterations finished qdiffx linear iterations at : 15:41:25 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 5.6403300E-05 7.2898865E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 15:41:25 3.600u 0.175s 0:04.07 92.6% 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 Sun Oct 9 2011 at 15:41:25 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5659 !!! WARNING: HIR 201 has a net charge of 0.5140 !!! WARNING: HIR 748 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.515969 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): 67.29600 137.7460 ymin,ymax (A): -6.234000 56.98200 zmin,zma (A): -3.312000 65.75400 x,y,z range (A): 70.44999 63.21600 69.06599 scale (grids/A): 1.515969 object centre (A): 102.5210 25.37400 31.22100 number of atom coordinates read : 5659 total number of charged atoms : 5488 net assigned charge : -3.471964 assigned positive charge : 868.0021 centred at (gu) : 89.83488 92.51836 90.73111 assigned negative charge : -871.4819 centred at (gu) : 90.01556 92.30194 91.03061 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 100937 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44364 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 29196 mr = 71593 m= 2461 mr = 20037 m= 40 mr = 1115 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3435 time to turn everything in is 0.4900000 number of dielectric boundary points 39889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 581 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 41063 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) : 0.5053230 object centre at (A) : 102.5210 25.37400 31.22100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2092808E-03 1.1234569E-03 midg,1,midg; midg,igrid,midg -1.1921784E-02 6.1815917E-03 1,midg,midg; igrid,midg,midg -1.7361805E-02 -1.0028938E-02 gauss-seidel spectral radius is 0.9981312 estimated iterations to convergence 184 setup time was (sec) 0.6900000 now iterating at: 15:41:26 rms-change max change #iterations 4.169677 164.3625 at 10iterations 1.717480 52.22075 at 20iterations 0.7060852 20.82571 at 30iterations 0.2916826 9.015945 at 40iterations 0.1205379 3.903507 at 50iterations 4.9854703E-02 1.372473 at 60iterations 2.0634910E-02 0.6270056 at 70iterations 8.5580265E-03 0.2513762 at 80iterations 3.5689939E-03 0.1128187 at 90iterations 1.5170545E-03 4.3792725E-02 at 100iterations 6.5947708E-04 2.1678925E-02 at 110iterations 3.0270155E-04 9.2124939E-03 at 120iterations finished qdiffx linear iterations at : 15:41:33 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 3.0270155E-04 9.2124939E-03 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 15:41:34 7.998u 0.215s 0:08.53 96.1% 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 Sun Oct 9 2011 at 15:41:34 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5659 !!! WARNING: HIR 201 has a net charge of 0.5140 !!! WARNING: HIR 748 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.273953 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): 67.29600 137.7460 ymin,ymax (A): -6.234000 56.98200 zmin,zma (A): -3.312000 65.75400 x,y,z range (A): 70.44999 63.21600 69.06599 scale (grids/A): 2.273953 object centre (A): 102.5210 25.37400 31.22100 number of atom coordinates read : 5659 total number of charged atoms : 5488 net assigned charge : -3.471964 assigned positive charge : 868.0021 centred at (gu) : 89.75193 93.77702 91.09642 assigned negative charge : -871.4819 centred at (gu) : 90.02335 93.45307 91.54572 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 235882 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44364 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 105335 mr = 175985 m= 26754 mr = 83598 m= 3600 mr = 19895 m= 168 mr = 2237 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 11608 time to turn everything in is 1.200000 number of dielectric boundary points 89983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 43765 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) : 1.515969 object centre at (A) : 102.5210 25.37400 31.22100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2248433E-02 0.1420193 midg,1,midg; midg,igrid,midg -0.2569477 0.2188225 1,midg,midg; igrid,midg,midg -0.5185252 0.1149841 gauss-seidel spectral radius is 0.9991778 estimated iterations to convergence 275 setup time was (sec) 1.450000 now iterating at: 15:41:36 rms-change max change #iterations 11.16475 328.9309 at 10iterations 6.403605 138.8288 at 20iterations 3.639301 82.18617 at 30iterations 2.061234 44.72971 at 40iterations 1.163761 31.45025 at 50iterations 0.6561337 13.22433 at 60iterations 0.3683979 7.275513 at 70iterations 0.2070647 3.486477 at 80iterations 0.1158758 2.190221 at 90iterations 6.4945720E-02 1.301079 at 100iterations 3.6322869E-02 0.6634140 at 110iterations 2.0312279E-02 0.3958111 at 120iterations 1.1368188E-02 0.1922045 at 130iterations 6.3476786E-03 0.1080341 at 140iterations 3.5574657E-03 5.9413910E-02 at 150iterations 1.9914452E-03 3.2654762E-02 at 160iterations 1.1185565E-03 2.0450592E-02 at 170iterations 6.2796951E-04 1.1373520E-02 at 180iterations finished qdiffx linear iterations at : 15:41:47 total time elapsed so far: 13.11000 # loops : 180 mean,max change (kT/e) : 6.2796951E-04 1.1373520E-02 energy calculations done at 13.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.24000 DelPhi exited at 15:41:48 13.246u 0.196s 0:13.76 97.6% 0+0k 0+0io 0pf+0w