Mon Oct 10 10:08:04 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 Mon Oct 10 2011 at 10:08:04 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2736 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5723565 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): -39.82900 22.37000 ymin,ymax (A): -46.00000 11.49200 zmin,zma (A): -1.607000 51.34400 x,y,z range (A): 62.19900 57.49200 52.95100 scale (grids/A): 0.5723565 object centre (A): -8.729499 -17.25400 24.86850 number of atom coordinates read : 2736 total number of charged atoms : 2610 net assigned charge : 9.014029 assigned positive charge : 405.5800 centred at (gu) : 87.74096 88.96292 86.85513 assigned negative charge : -396.5665 centred at (gu) : 87.69061 88.92252 86.71664 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5961 nv = 96 ne = 84 npr = 52828 no. pairs analyzed = 52828 no. exposed pairs = 4042 no. arc points = 29326 no. surface atoms = 1341 nbur = 1395 mkacc time = 0.1200000 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= 283 mr = 2650 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3583 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2901 ## 327 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7641 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2432980E-09 1.7362629E-09 midg,1,midg; midg,igrid,midg 1.2273157E-09 1.7086800E-09 1,midg,midg; igrid,midg,midg 1.3605465E-09 1.3777889E-09 gauss-seidel spectral radius is 0.9842411 estimated iterations to convergence 65 setup time was (sec) 0.5500000 now iterating at: 10:08:05 rms-change max change #iterations 8.8326521E-02 15.06195 at 10iterations 6.6624866E-03 1.230148 at 20iterations 4.9869693E-04 8.2759857E-02 at 30iterations 4.1754149E-05 7.0514679E-03 at 40iterations 4.7895837E-06 5.7983398E-04 at 50iterations finished qdiffx linear iterations at : 10:08:07 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 4.7895837E-06 5.7983398E-04 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 10:08:08 3.387u 0.142s 0:03.99 88.2% 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 10:08:08 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2736 !!! WARNING: HIT 235 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.717070 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): -39.82900 22.37000 ymin,ymax (A): -46.00000 11.49200 zmin,zma (A): -1.607000 51.34400 x,y,z range (A): 62.19900 57.49200 52.95100 scale (grids/A): 1.717070 object centre (A): -8.729499 -17.25400 24.86850 number of atom coordinates read : 2736 total number of charged atoms : 2610 net assigned charge : 9.014029 assigned positive charge : 405.5800 centred at (gu) : 83.22250 86.88831 80.56504 assigned negative charge : -396.5665 centred at (gu) : 83.07161 86.76734 80.14957 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 63901 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29326 grid for indexing accessible points = 1.400000 m= 19863 mr = 39092 m= 2416 mr = 12619 m= 92 mr = 1108 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 33446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 20242 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) : 0.5723565 object centre at (A) : -8.729499 -17.25400 24.86850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6676756E-03 1.1160685E-02 midg,1,midg; midg,igrid,midg 6.8851425E-03 1.6666250E-02 1,midg,midg; igrid,midg,midg 1.1725196E-02 -1.5014409E-02 gauss-seidel spectral radius is 0.9983467 estimated iterations to convergence 195 setup time was (sec) 0.7800000 now iterating at: 10:08:09 rms-change max change #iterations 3.465105 144.6339 at 10iterations 1.492428 61.36762 at 20iterations 0.6437862 21.99101 at 30iterations 0.2785422 10.23888 at 40iterations 0.1202473 4.774611 at 50iterations 5.1926490E-02 2.039639 at 60iterations 2.2467740E-02 0.7637081 at 70iterations 9.7425645E-03 0.3674088 at 80iterations 4.2081336E-03 0.1537876 at 90iterations 1.8193068E-03 6.4577103E-02 at 100iterations 7.9091475E-04 2.7246952E-02 at 110iterations 3.4170822E-04 1.4228821E-02 at 120iterations finished qdiffx linear iterations at : 10:08:16 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 3.4170822E-04 1.4228821E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 10:08:16 7.508u 0.165s 0:07.96 96.2% 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 10:08:16 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2736 !!! WARNING: HIT 235 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.575604 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): -39.82900 22.37000 ymin,ymax (A): -46.00000 11.49200 zmin,zma (A): -1.607000 51.34400 x,y,z range (A): 62.19900 57.49200 52.95100 scale (grids/A): 2.575604 object centre (A): -8.729499 -17.25400 24.86850 number of atom coordinates read : 2736 total number of charged atoms : 2610 net assigned charge : 9.014029 assigned positive charge : 405.5800 centred at (gu) : 79.83372 85.33235 75.84734 assigned negative charge : -396.5665 centred at (gu) : 79.60734 85.15093 75.22436 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 147543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29326 grid for indexing accessible points = 1.400000 m= 66020 mr = 96351 m= 20428 mr = 49373 m= 3931 mr = 14511 m= 378 mr = 2361 m= 22 mr = 174 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 75552 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 20869 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) : 1.717070 object centre at (A) : -8.729499 -17.25400 24.86850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1286682 0.1137055 midg,1,midg; midg,igrid,midg 8.6551113E-03 0.2863041 1,midg,midg; igrid,midg,midg 0.2298846 -0.5616569 gauss-seidel spectral radius is 0.9991907 estimated iterations to convergence 278 setup time was (sec) 1.470000 now iterating at: 10:08:18 rms-change max change #iterations 9.029894 309.5439 at 10iterations 5.268943 150.9286 at 20iterations 3.033533 81.42938 at 30iterations 1.731137 46.82674 at 40iterations 0.9832556 26.71820 at 50iterations 0.5589718 14.58639 at 60iterations 0.3154600 7.528870 at 70iterations 0.1775735 3.960899 at 80iterations 0.1000509 2.304161 at 90iterations 5.6347452E-02 1.253254 at 100iterations 3.1531386E-02 0.7100801 at 110iterations 1.7702727E-02 0.3853302 at 120iterations 9.9091502E-03 0.2223320 at 130iterations 5.5524241E-03 0.1198564 at 140iterations 3.1080649E-03 6.8827152E-02 at 150iterations 1.7409959E-03 3.7860870E-02 at 160iterations 9.7377063E-04 2.1978378E-02 at 170iterations 5.4717291E-04 1.0622978E-02 at 180iterations finished qdiffx linear iterations at : 10:08:28 total time elapsed so far: 11.67000 # loops : 180 mean,max change (kT/e) : 5.4717291E-04 1.0622978E-02 energy calculations done at 11.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.86000 DelPhi exited at 10:08:29 11.865u 0.175s 0:12.35 97.4% 0+0k 0+0io 0pf+0w