Sat Oct 8 15:02:19 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 15:02:19 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3266 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: 0.6041783 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): -1.607000 57.31600 ymin,ymax (A): -24.33900 27.20200 zmin,zma (A): -9.550000 45.61200 x,y,z range (A): 58.92300 51.54100 55.16200 scale (grids/A): 0.6041783 object centre (A): 27.85450 1.431500 18.03100 number of atom coordinates read : 3266 total number of charged atoms : 3120 net assigned charge : 3.500014 assigned positive charge : 489.6437 centred at (gu) : 92.04487 89.23906 90.07034 assigned negative charge : -486.1451 centred at (gu) : 92.09029 89.27020 90.09720 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7850 nv = 96 ne = 84 npr = 67549 no. pairs analyzed = 67549 no. exposed pairs = 3718 no. arc points = 26120 no. surface atoms = 1268 nbur = 1998 mkacc time = 0.1800000 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 = 1.456000 m= 373 mr = 4507 m= 0 mr = 29 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.3700000 number of dielectric boundary points 3687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2682 ## 259 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9852 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0847920E-09 3.6046718E-10 midg,1,midg; midg,igrid,midg 3.9786459E-09 1.2535795E-10 1,midg,midg; igrid,midg,midg 2.5940947E-09 -1.0518483E-09 gauss-seidel spectral radius is 0.9858699 estimated iterations to convergence 69 setup time was (sec) 0.6600000 now iterating at: 15:02:20 rms-change max change #iterations 0.1271591 16.56645 at 10iterations 1.1432905E-02 1.488400 at 20iterations 1.1220846E-03 0.1531639 at 30iterations 1.5230640E-04 2.1030426E-02 at 40iterations 3.3787364E-05 5.6500435E-03 at 50iterations finished qdiffx linear iterations at : 15:02:24 total time elapsed so far: 4.440000 # loops : 50 mean,max change (kT/e) : 3.3787364E-05 5.6500435E-03 energy calculations done at 4.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 15:02:24 4.622u 0.405s 0:05.31 94.5% 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 15:02:24 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3266 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: 1.812535 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): -1.607000 57.31600 ymin,ymax (A): -24.33900 27.20200 zmin,zma (A): -9.550000 45.61200 x,y,z range (A): 58.92300 51.54100 55.16200 scale (grids/A): 1.812535 object centre (A): 27.85450 1.431500 18.03100 number of atom coordinates read : 3266 total number of charged atoms : 3120 net assigned charge : 3.500014 assigned positive charge : 489.6437 centred at (gu) : 96.13348 87.71607 90.20986 assigned negative charge : -486.1451 centred at (gu) : 96.27064 87.81026 90.29132 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 86064 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26120 grid for indexing accessible points = 1.400000 m= 30015 mr = 61716 m= 4065 mr = 22211 m= 168 mr = 2435 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1880 time to turn everything in is 0.6800000 number of dielectric boundary points 33899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 24425 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) : 0.6041783 object centre at (A) : 27.85450 1.431500 18.03100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4086588E-03 -1.9633161E-02 midg,1,midg; midg,igrid,midg 7.8991475E-03 7.3309718E-03 1,midg,midg; igrid,midg,midg 3.3329766E-02 1.3094236E-02 gauss-seidel spectral radius is 0.9985538 estimated iterations to convergence 208 setup time was (sec) 1.020000 now iterating at: 15:02:26 rms-change max change #iterations 4.352694 176.8848 at 10iterations 1.977906 63.82674 at 20iterations 0.9112631 30.23561 at 30iterations 0.4175522 13.22460 at 40iterations 0.1918991 6.240630 at 50iterations 8.8165514E-02 2.496255 at 60iterations 4.0395036E-02 1.247242 at 70iterations 1.8554391E-02 0.5492449 at 80iterations 8.5203266E-03 0.2787828 at 90iterations 3.9335419E-03 0.1159389 at 100iterations 1.8055364E-03 5.2676201E-02 at 110iterations 8.3475735E-04 2.4139404E-02 at 120iterations finished qdiffx linear iterations at : 15:02:36 total time elapsed so far: 10.73000 # loops : 120 mean,max change (kT/e) : 8.3475735E-04 2.4139404E-02 energy calculations done at 10.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.90000 DelPhi exited at 15:02:36 10.907u 0.459s 0:11.75 96.5% 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 15:02:36 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3266 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.718802 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): -1.607000 57.31600 ymin,ymax (A): -24.33900 27.20200 zmin,zma (A): -9.550000 45.61200 x,y,z range (A): 58.92300 51.54100 55.16200 scale (grids/A): 2.718802 object centre (A): 27.85450 1.431500 18.03100 number of atom coordinates read : 3266 total number of charged atoms : 3120 net assigned charge : 3.500014 assigned positive charge : 489.6437 centred at (gu) : 99.20002 86.57397 90.31467 assigned negative charge : -486.1451 centred at (gu) : 99.40594 86.71539 90.43693 start vw surface at 0.1400000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 199521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26120 grid for indexing accessible points = 1.400000 m= 99926 mr = 149404 m= 33391 mr = 82344 m= 7045 mr = 26723 m= 755 mr = 5263 m= 32 mr = 475 m= 0 mr = 15 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 6373 time to turn everything in is 1.780000 number of dielectric boundary points 76446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 24956 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) : 1.812535 object centre at (A) : 27.85450 1.431500 18.03100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7566930E-02 -0.2731972 midg,1,midg; midg,igrid,midg 5.1349690E-03 0.1006121 1,midg,midg; igrid,midg,midg 0.4312384 0.2751580 gauss-seidel spectral radius is 0.9992456 estimated iterations to convergence 287 setup time was (sec) 2.110000 now iterating at: 15:02:39 rms-change max change #iterations 10.39600 312.0527 at 10iterations 6.028832 115.3342 at 20iterations 3.470598 65.93602 at 30iterations 1.997576 34.13218 at 40iterations 1.145753 20.60660 at 50iterations 0.6564844 12.05104 at 60iterations 0.3764271 6.266973 at 70iterations 0.2152050 3.791115 at 80iterations 0.1230957 2.344534 at 90iterations 7.0342109E-02 1.196677 at 100iterations 4.0283095E-02 0.7333221 at 110iterations 2.3091808E-02 0.3825264 at 120iterations 1.3190254E-02 0.2241745 at 130iterations 7.5652222E-03 0.1390610 at 140iterations 4.3490035E-03 7.7209473E-02 at 150iterations 2.5004777E-03 4.3151855E-02 at 160iterations 1.4455288E-03 2.4578691E-02 at 170iterations 8.4175472E-04 1.3824463E-02 at 180iterations finished qdiffx linear iterations at : 15:02:55 total time elapsed so far: 18.18000 # loops : 180 mean,max change (kT/e) : 8.4175472E-04 1.3824463E-02 energy calculations done at 18.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.35000 DelPhi exited at 15:02:55 18.353u 0.487s 0:19.15 98.3% 0+0k 0+0io 0pf+0w