Sun Oct 9 19:11:59 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 19:11:59 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4727 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5571205 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): 3.230000 64.59300 ymin,ymax (A): -8.313000 52.37900 zmin,zma (A): -2.263000 61.63700 x,y,z range (A): 61.36300 60.69200 63.90000 scale (grids/A): 0.5571205 object centre (A): 33.91150 22.03300 29.68700 number of atom coordinates read : 4727 total number of charged atoms : 4580 net assigned charge : 2.254029 assigned positive charge : 725.8132 centred at (gu) : 88.17313 89.34988 89.43147 assigned negative charge : -723.5639 centred at (gu) : 88.07941 89.39021 89.38702 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 9831 nv = 96 ne = 84 npr = 93632 no. pairs analyzed = 93632 no. exposed pairs = 5700 no. arc points = 38389 no. surface atoms = 1946 nbur = 2781 mkacc time = 0.2500000 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 = 1.540000 m= 447 mr = 5561 m= 4 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3991 ## 448 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 12705 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5179949E-10 8.3718327E-10 midg,1,midg; midg,igrid,midg 1.0502343E-09 -3.4796990E-10 1,midg,midg; igrid,midg,midg -2.0432136E-09 1.1197511E-09 gauss-seidel spectral radius is 0.9835178 estimated iterations to convergence 64 setup time was (sec) 0.8700000 now iterating at: 19:12:01 rms-change max change #iterations 0.1113876 15.85645 at 10iterations 1.4478588E-02 1.969109 at 20iterations 5.9167836E-03 0.7914505 at 30iterations 2.8742603E-03 0.3834915 at 40iterations 1.4097536E-03 0.1848145 at 50iterations finished qdiffx linear iterations at : 19:12:05 total time elapsed so far: 5.370000 # loops : 50 mean,max change (kT/e) : 1.4097536E-03 0.1848145 energy calculations done at 5.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.540000 DelPhi exited at 19:12:06 5.547u 0.452s 0:06.30 95.0% 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 Sun Oct 9 2011 at 19:12:06 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4727 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.671361 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): 3.230000 64.59300 ymin,ymax (A): -8.313000 52.37900 zmin,zma (A): -2.263000 61.63700 x,y,z range (A): 61.36300 60.69200 63.90000 scale (grids/A): 1.671361 object centre (A): 33.91150 22.03300 29.68700 number of atom coordinates read : 4727 total number of charged atoms : 4580 net assigned charge : 2.254029 assigned positive charge : 725.8132 centred at (gu) : 84.51776 88.04827 88.29353 assigned negative charge : -723.5639 centred at (gu) : 84.23808 88.17080 88.16081 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 109517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38389 grid for indexing accessible points = 1.400000 m= 39361 mr = 79061 m= 5011 mr = 28649 m= 149 mr = 2669 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 43652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 374 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 35300 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) : 0.5571205 object centre at (A) : 33.91150 22.03300 29.68700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1259250E-02 -4.8483857E-03 midg,1,midg; midg,igrid,midg 1.6231762E-02 1.0325407E-02 1,midg,midg; igrid,midg,midg -8.5641356E-04 1.6183658E-02 gauss-seidel spectral radius is 0.9984428 estimated iterations to convergence 201 setup time was (sec) 1.310000 now iterating at: 19:12:07 rms-change max change #iterations 4.702762 148.3709 at 10iterations 2.093377 63.51051 at 20iterations 0.9328232 27.30296 at 30iterations 0.4175001 13.20914 at 40iterations 0.1868607 5.940786 at 50iterations 8.5031800E-02 2.416504 at 60iterations 4.0037520E-02 1.480270 at 70iterations 2.0424997E-02 0.6262817 at 80iterations 1.1856215E-02 0.3753548 at 90iterations 7.9589728E-03 0.2529755 at 100iterations 5.8182166E-03 0.1808739 at 110iterations 4.4234763E-03 0.1273499 at 120iterations finished qdiffx linear iterations at : 19:12:19 total time elapsed so far: 13.14000 # loops : 120 mean,max change (kT/e) : 4.4234763E-03 0.1273499 energy calculations done at 13.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.30000 DelPhi exited at 19:12:20 13.306u 0.508s 0:14.09 97.9% 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 19:12:20 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4727 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.507042 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): 3.230000 64.59300 ymin,ymax (A): -8.313000 52.37900 zmin,zma (A): -2.263000 61.63700 x,y,z range (A): 61.36300 60.69200 63.90000 scale (grids/A): 2.507042 object centre (A): 33.91150 22.03300 29.68700 number of atom coordinates read : 4727 total number of charged atoms : 4580 net assigned charge : 2.254029 assigned positive charge : 725.8132 centred at (gu) : 81.77651 87.07242 87.43974 assigned negative charge : -723.5639 centred at (gu) : 81.35709 87.25628 87.24134 start vw surface at 0.1700000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 254447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38389 grid for indexing accessible points = 1.400000 m= 131221 mr = 192477 m= 42990 mr = 107188 m= 8127 mr = 33536 m= 647 mr = 5576 m= 17 mr = 320 m= 0 mr = 2 time to grow re-entrant surface = 1.510000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.340000 number of dielectric boundary points 98350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 2.500000 number of grid points assigned charge 36598 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) : 1.671361 object centre at (A) : 33.91150 22.03300 29.68700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3685783 2.1884596E-02 midg,1,midg; midg,igrid,midg 6.5969102E-02 -2.5146868E-02 1,midg,midg; igrid,midg,midg -7.6476619E-02 0.2538598 gauss-seidel spectral radius is 0.9992527 estimated iterations to convergence 289 setup time was (sec) 2.730000 now iterating at: 19:12:23 rms-change max change #iterations 11.92039 341.0648 at 10iterations 7.013942 147.5693 at 20iterations 4.108204 95.58325 at 30iterations 2.389483 45.31918 at 40iterations 1.390954 25.38466 at 50iterations 0.8056625 14.53040 at 60iterations 0.4659779 8.888981 at 70iterations 0.2692260 4.536224 at 80iterations 0.1560590 2.517361 at 90iterations 9.0291277E-02 1.608948 at 100iterations 5.2803706E-02 1.000965 at 110iterations 3.1432807E-02 0.5364609 at 120iterations 1.9321693E-02 0.3356400 at 130iterations 1.2570312E-02 0.2311859 at 140iterations 8.7810922E-03 0.1714096 at 150iterations 6.6008917E-03 0.1248245 at 160iterations 5.2503906E-03 9.1880798E-02 at 170iterations 4.3271813E-03 7.7621460E-02 at 180iterations finished qdiffx linear iterations at : 19:12:44 total time elapsed so far: 23.51000 # loops : 180 mean,max change (kT/e) : 4.3271813E-03 7.7621460E-02 energy calculations done at 23.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.67000 DelPhi exited at 19:12:45 23.677u 0.606s 0:24.67 98.3% 0+0k 0+0io 0pf+0w