Sat Oct 8 14:19:58 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 14:19:58 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 = 3033 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6248025 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): -14.34800 35.32200 ymin,ymax (A): -12.13500 44.84300 zmin,zma (A): -40.01600 12.66200 x,y,z range (A): 49.67000 56.97800 52.67800 scale (grids/A): 0.6248025 object centre (A): 10.48700 16.35400 -13.67700 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : 7.1674585E-06 assigned positive charge : 454.5165 centred at (gu) : 91.76933 91.86136 91.12492 assigned negative charge : -454.5173 centred at (gu) : 91.81820 91.78170 91.19173 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7771 nv = 96 ne = 84 npr = 63635 no. pairs analyzed = 63635 no. exposed pairs = 3486 no. arc points = 24379 no. surface atoms = 1195 nbur = 1838 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 353 mr = 4474 m= 3 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2100000 number of dielectric boundary points 3610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2368 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9589 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5952726E-09 -7.6532940E-09 midg,1,midg; midg,igrid,midg -4.7096247E-09 1.0671468E-08 1,midg,midg; igrid,midg,midg 2.9280678E-09 -6.4595427E-09 gauss-seidel spectral radius is 0.9867635 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 14:19:58 rms-change max change #iterations 0.1444910 20.33894 at 10iterations 1.3987727E-02 1.781326 at 20iterations 1.4303464E-03 0.2219648 at 30iterations 1.8144521E-04 2.4707794E-02 at 40iterations 3.1591022E-05 4.4708252E-03 at 50iterations finished qdiffx linear iterations at : 14:20:01 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 3.1591022E-05 4.4708252E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:20:01 3.356u 0.181s 0:03.83 92.1% 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 8 2011 at 14:20:01 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 = 3033 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.874408 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): -14.34800 35.32200 ymin,ymax (A): -12.13500 44.84300 zmin,zma (A): -40.01600 12.66200 x,y,z range (A): 49.67000 56.97800 52.67800 scale (grids/A): 1.874408 object centre (A): 10.48700 16.35400 -13.67700 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : 7.1674585E-06 assigned positive charge : 454.5165 centred at (gu) : 95.30746 95.58347 93.37440 assigned negative charge : -454.5173 centred at (gu) : 95.45449 95.34477 93.57479 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85122 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24379 grid for indexing accessible points = 1.400000 m= 30034 mr = 61226 m= 4144 mr = 22401 m= 196 mr = 2461 m= 3 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 33358 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 22649 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) : 0.6248025 object centre at (A) : 10.48700 16.35400 -13.67700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3447003E-02 7.5904476E-03 midg,1,midg; midg,igrid,midg -1.3853791E-02 4.8105292E-02 1,midg,midg; igrid,midg,midg 7.0837331E-03 -1.2108023E-02 gauss-seidel spectral radius is 0.9986261 estimated iterations to convergence 214 setup time was (sec) 0.6200000 now iterating at: 14:20:02 rms-change max change #iterations 4.533506 164.4836 at 10iterations 2.117098 62.09171 at 20iterations 0.9897850 30.01604 at 30iterations 0.4631424 13.39301 at 40iterations 0.2171795 5.905054 at 50iterations 0.1020151 3.008096 at 60iterations 4.7774293E-02 1.516533 at 70iterations 2.2361616E-02 0.6913443 at 80iterations 1.0484177E-02 0.3022766 at 90iterations 4.9133613E-03 0.1401567 at 100iterations 2.3078006E-03 6.8654060E-02 at 110iterations 1.0810083E-03 3.3081055E-02 at 120iterations finished qdiffx linear iterations at : 14:20:09 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.0810083E-03 3.3081055E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 14:20:10 7.749u 0.183s 0:08.29 95.5% 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 8 2011 at 14:20:10 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 = 3033 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.811611 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): -14.34800 35.32200 ymin,ymax (A): -12.13500 44.84300 zmin,zma (A): -40.01600 12.66200 x,y,z range (A): 49.67000 56.97800 52.67800 scale (grids/A): 2.811611 object centre (A): 10.48700 16.35400 -13.67700 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : 7.1674585E-06 assigned positive charge : 454.5165 centred at (gu) : 97.96109 98.37513 95.06136 assigned negative charge : -454.5173 centred at (gu) : 98.18165 98.01711 95.36224 start vw surface at 0.1000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 197568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24379 grid for indexing accessible points = 1.400000 m= 99531 mr = 148426 m= 33764 mr = 82480 m= 7214 mr = 27059 m= 881 mr = 5275 m= 42 mr = 522 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 75231 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 23083 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) : 1.874408 object centre at (A) : 10.48700 16.35400 -13.67700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1289563 0.2183158 midg,1,midg; midg,igrid,midg -8.9373790E-02 0.6917011 1,midg,midg; igrid,midg,midg 0.1143738 -0.1006031 gauss-seidel spectral radius is 0.9992605 estimated iterations to convergence 290 setup time was (sec) 1.290000 now iterating at: 14:20:11 rms-change max change #iterations 10.57407 289.9118 at 10iterations 6.188564 125.6662 at 20iterations 3.603662 71.42570 at 30iterations 2.087591 39.18086 at 40iterations 1.210049 20.48870 at 50iterations 0.6981466 12.96833 at 60iterations 0.4044972 6.789081 at 70iterations 0.2332211 4.110796 at 80iterations 0.1344320 2.418909 at 90iterations 7.7431157E-02 1.330730 at 100iterations 4.4498283E-02 0.8025555 at 110iterations 2.5675317E-02 0.4643607 at 120iterations 1.4772221E-02 0.2644005 at 130iterations 8.5122529E-03 0.1442771 at 140iterations 4.9003153E-03 8.0554962E-02 at 150iterations 2.8249428E-03 4.8053741E-02 at 160iterations 1.6286724E-03 2.7881622E-02 at 170iterations 9.3798520E-04 1.5209198E-02 at 180iterations finished qdiffx linear iterations at : 14:20:23 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 9.3798520E-04 1.5209198E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 14:20:23 12.742u 0.200s 0:13.24 97.7% 0+0k 0+0io 0pf+0w