Tue Oct 11 06:38:24 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 Tue Oct 11 2011 at 06:38:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2040 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: 0.7091492 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): -20.17600 24.67300 ymin,ymax (A): -28.57100 11.16200 zmin,zma (A): -13.50300 36.69800 x,y,z range (A): 44.84900 39.73300 50.20100 scale (grids/A): 0.7091492 object centre (A): 2.248501 -8.704500 11.59750 number of atom coordinates read : 2040 total number of charged atoms : 1912 net assigned charge : 7.500009 assigned positive charge : 309.1790 centred at (gu) : 89.88813 90.56005 89.46832 assigned negative charge : -301.6792 centred at (gu) : 89.71020 90.53889 89.43249 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6931 nv = 96 ne = 84 npr = 41051 no. pairs analyzed = 41051 no. exposed pairs = 2465 no. arc points = 16711 no. surface atoms = 834 nbur = 1206 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 3990 m= 5 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1613 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7722 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3200065E-08 7.5803293E-08 midg,1,midg; midg,igrid,midg 5.0117517E-08 8.5177248E-08 1,midg,midg; igrid,midg,midg -2.4467344E-08 1.4963108E-07 gauss-seidel spectral radius is 0.9896287 estimated iterations to convergence 80 setup time was (sec) 0.4600000 now iterating at: 06:38:25 rms-change max change #iterations 0.1976880 28.16913 at 10iterations 2.4737751E-02 3.216597 at 20iterations 3.2073434E-03 0.4236031 at 30iterations 4.6343962E-04 6.2595367E-02 at 40iterations 9.6091288E-05 1.2144089E-02 at 50iterations finished qdiffx linear iterations at : 06:38:27 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 9.6091288E-05 1.2144089E-02 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 06:38:28 3.049u 0.133s 0:03.50 90.5% 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 Tue Oct 11 2011 at 06:38:28 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 = 2040 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: 2.127448 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): -20.17600 24.67300 ymin,ymax (A): -28.57100 11.16200 zmin,zma (A): -13.50300 36.69800 x,y,z range (A): 44.84900 39.73300 50.20100 scale (grids/A): 2.127448 object centre (A): 2.248501 -8.704500 11.59750 number of atom coordinates read : 2040 total number of charged atoms : 1912 net assigned charge : 7.500009 assigned positive charge : 309.1790 centred at (gu) : 89.66440 91.68032 88.40495 assigned negative charge : -301.6792 centred at (gu) : 89.13074 91.61678 88.29764 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73792 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16711 grid for indexing accessible points = 1.400000 m= 29286 mr = 52710 m= 5617 mr = 22222 m= 491 mr = 3677 m= 11 mr = 267 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 30321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 15207 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) : 0.7091492 object centre at (A) : 2.248501 -8.704500 11.59750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4925089E-02 5.0764915E-02 midg,1,midg; midg,igrid,midg 5.4970696E-03 3.4163002E-02 1,midg,midg; igrid,midg,midg 1.7075639E-02 4.0050231E-02 gauss-seidel spectral radius is 0.9988307 estimated iterations to convergence 231 setup time was (sec) 0.7900000 now iterating at: 06:38:29 rms-change max change #iterations 4.522556 169.2322 at 10iterations 2.232609 88.82880 at 20iterations 1.112182 34.19949 at 30iterations 0.5504604 17.71438 at 40iterations 0.2737187 8.625261 at 50iterations 0.1359603 4.228165 at 60iterations 6.7621261E-02 1.996682 at 70iterations 3.3691477E-02 0.9665489 at 80iterations 1.6771650E-02 0.5087433 at 90iterations 8.3925137E-03 0.2626877 at 100iterations 4.1979118E-03 0.1330824 at 110iterations 2.1330754E-03 7.9154968E-02 at 120iterations finished qdiffx linear iterations at : 06:38:35 total time elapsed so far: 6.990000 # loops : 120 mean,max change (kT/e) : 2.1330754E-03 7.9154968E-02 energy calculations done at 6.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.210000 DelPhi exited at 06:38:35 7.208u 0.144s 0:07.64 96.0% 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 Tue Oct 11 2011 at 06:38:35 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 = 2040 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: 3.191171 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): -20.17600 24.67300 ymin,ymax (A): -28.57100 11.16200 zmin,zma (A): -13.50300 36.69800 x,y,z range (A): 44.84900 39.73300 50.20100 scale (grids/A): 3.191171 object centre (A): 2.248501 -8.704500 11.59750 number of atom coordinates read : 2040 total number of charged atoms : 1912 net assigned charge : 7.500009 assigned positive charge : 309.1790 centred at (gu) : 89.49656 92.52047 87.60745 assigned negative charge : -301.6792 centred at (gu) : 88.69624 92.42522 87.44652 start vw surface at 0.1400000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 170051 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16711 grid for indexing accessible points = 1.400000 m= 91678 mr = 126826 m= 36902 mr = 76238 m= 10446 mr = 30243 m= 2047 mr = 8016 m= 233 mr = 1490 m= 4 mr = 145 m= 0 mr = 2 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.650000 number of dielectric boundary points 68401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 15296 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) : 2.127448 object centre at (A) : 2.248501 -8.704500 11.59750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7157933 0.4060213 midg,1,midg; midg,igrid,midg 2.5909569E-02 0.2716103 1,midg,midg; igrid,midg,midg 0.2661846 0.3026379 gauss-seidel spectral radius is 0.9992907 estimated iterations to convergence 296 setup time was (sec) 1.930000 now iterating at: 06:38:37 rms-change max change #iterations 10.12479 378.5895 at 10iterations 5.982217 136.6577 at 20iterations 3.527364 72.97970 at 30iterations 2.077060 37.68734 at 40iterations 1.220989 24.02906 at 50iterations 0.7170091 14.36869 at 60iterations 0.4210018 7.754759 at 70iterations 0.2459983 4.744224 at 80iterations 0.1442607 2.690747 at 90iterations 8.4276840E-02 1.536056 at 100iterations 4.9340729E-02 0.9254999 at 110iterations 2.8939890E-02 0.4920998 at 120iterations 1.7052770E-02 0.2864017 at 130iterations 1.0105086E-02 0.1842499 at 140iterations 6.0792477E-03 0.1098328 at 150iterations 3.7431214E-03 6.9408417E-02 at 160iterations 2.4052593E-03 4.8637390E-02 at 170iterations 1.6260310E-03 2.9594421E-02 at 180iterations finished qdiffx linear iterations at : 06:38:47 total time elapsed so far: 11.74000 # loops : 180 mean,max change (kT/e) : 1.6260310E-03 2.9594421E-02 energy calculations done at 11.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 06:38:48 11.912u 0.166s 0:12.39 97.4% 0+0k 0+0io 0pf+0w