Sat Oct 15 14:32:07 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 15 2011 at 14:32:11 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 = 1700 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6656694 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): -31.18000 22.30000 ymin,ymax (A): 10.57700 51.46200 zmin,zma (A): 26.51800 69.53201 x,y,z range (A): 53.48000 40.88500 43.01401 scale (grids/A): 0.6656694 object centre (A): -4.440001 31.01950 48.02500 number of atom coordinates read : 1700 total number of charged atoms : 1571 net assigned charge : 6.500028 assigned positive charge : 248.5584 centred at (gu) : 90.83941 90.02071 91.18649 assigned negative charge : -242.0585 centred at (gu) : 90.84246 90.05751 91.13028 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5072 nv = 96 ne = 84 npr = 33614 no. pairs analyzed = 33614 no. exposed pairs = 2295 no. arc points = 16593 no. surface atoms = 769 nbur = 931 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 2452 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1537 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 5793 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8369614E-09 3.4458566E-08 midg,1,midg; midg,igrid,midg 2.4218231E-08 1.3904126E-08 1,midg,midg; igrid,midg,midg 1.6544092E-08 2.2075211E-08 gauss-seidel spectral radius is 0.9882286 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 14:32:13 rms-change max change #iterations 0.1311877 25.14143 at 10iterations 1.3904434E-02 2.945465 at 20iterations 1.4616773E-03 0.2386589 at 30iterations 1.5936313E-04 2.8959274E-02 at 40iterations 1.7196820E-05 2.5914907E-03 at 50iterations finished qdiffx linear iterations at : 14:32:28 total time elapsed so far: 5.340000 # loops : 50 mean,max change (kT/e) : 1.7196820E-05 2.5914907E-03 energy calculations done at 5.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.520000 DelPhi exited at 14:32:30 5.527u 0.453s 0:19.53 30.5% 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 15 2011 at 14:32:30 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 = 1700 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.997008 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): -31.18000 22.30000 ymin,ymax (A): 10.57700 51.46200 zmin,zma (A): 26.51800 69.53201 x,y,z range (A): 53.48000 40.88500 43.01401 scale (grids/A): 1.997008 object centre (A): -4.440001 31.01950 48.02500 number of atom coordinates read : 1700 total number of charged atoms : 1571 net assigned charge : 6.500028 assigned positive charge : 248.5584 centred at (gu) : 92.51831 90.06226 93.55992 assigned negative charge : -242.0585 centred at (gu) : 92.52781 90.17300 93.39143 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 53457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16593 grid for indexing accessible points = 1.400000 m= 18429 mr = 34023 m= 3361 mr = 12766 m= 241 mr = 2091 m= 0 mr = 86 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 26522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 12417 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) : 0.6656694 object centre at (A) : -4.440001 31.01950 48.02500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2255492E-03 1.2768605E-02 midg,1,midg; midg,igrid,midg 2.2515569E-02 4.3621007E-03 1,midg,midg; igrid,midg,midg 1.2489406E-02 6.7102513E-03 gauss-seidel spectral radius is 0.9986718 estimated iterations to convergence 217 setup time was (sec) 0.8500000 now iterating at: 14:32:35 rms-change max change #iterations 3.564040 170.0764 at 10iterations 1.678630 67.64989 at 20iterations 0.7896116 29.26132 at 30iterations 0.3737024 13.73169 at 40iterations 0.1763580 7.012676 at 50iterations 8.3351173E-02 3.005941 at 60iterations 3.9203275E-02 1.422434 at 70iterations 1.8474491E-02 0.6956940 at 80iterations 8.7234108E-03 0.3374767 at 90iterations 4.1236444E-03 0.1431313 at 100iterations 1.9500087E-03 7.0335388E-02 at 110iterations 9.1778947E-04 4.2137146E-02 at 120iterations finished qdiffx linear iterations at : 14:33:08 total time elapsed so far: 12.24000 # loops : 120 mean,max change (kT/e) : 9.1778947E-04 4.2137146E-02 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 14:33:09 12.416u 0.542s 0:39.23 33.0% 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 Sat Oct 15 2011 at 14:33:15 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 = 1700 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.995512 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): -31.18000 22.30000 ymin,ymax (A): 10.57700 51.46200 zmin,zma (A): 26.51800 69.53201 x,y,z range (A): 53.48000 40.88500 43.01401 scale (grids/A): 2.995512 object centre (A): -4.440001 31.01950 48.02500 number of atom coordinates read : 1700 total number of charged atoms : 1571 net assigned charge : 6.500028 assigned positive charge : 248.5584 centred at (gu) : 93.77759 90.09340 95.33999 assigned negative charge : -242.0585 centred at (gu) : 93.79182 90.25961 95.08723 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 123462 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16593 grid for indexing accessible points = 1.400000 m= 57677 mr = 83196 m= 22258 mr = 44942 m= 6157 mr = 17468 m= 978 mr = 4604 m= 64 mr = 617 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 59739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 12564 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) : 1.997008 object centre at (A) : -4.440001 31.01950 48.02500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1979502E-02 7.1648806E-03 midg,1,midg; midg,igrid,midg 0.2095685 -3.5986502E-02 1,midg,midg; igrid,midg,midg 0.1093754 2.1250132E-02 gauss-seidel spectral radius is 0.9992579 estimated iterations to convergence 290 setup time was (sec) 1.600000 now iterating at: 14:33:23 rms-change max change #iterations 8.313736 402.6645 at 10iterations 4.822546 160.5417 at 20iterations 2.799050 82.77341 at 30iterations 1.615926 44.63213 at 40iterations 0.9320268 19.13226 at 50iterations 0.5384507 11.78454 at 60iterations 0.3098100 7.117174 at 70iterations 0.1775590 3.994446 at 80iterations 0.1021068 2.056834 at 90iterations 5.8604583E-02 1.459373 at 100iterations 3.3658519E-02 0.7005100 at 110iterations 1.9319141E-02 0.4180083 at 120iterations 1.1085045E-02 0.2360840 at 130iterations 6.3560940E-03 0.1263275 at 140iterations 3.6432494E-03 7.7972412E-02 at 150iterations 2.0877598E-03 4.5957565E-02 at 160iterations 1.2005668E-03 2.5784492E-02 at 170iterations 6.8714883E-04 1.3117790E-02 at 180iterations finished qdiffx linear iterations at : 14:34:06 total time elapsed so far: 20.04000 # loops : 180 mean,max change (kT/e) : 6.8714883E-04 1.3117790E-02 energy calculations done at 20.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.22000 DelPhi exited at 14:34:07 20.229u 0.621s 0:51.94 40.1% 0+0k 0+0io 0pf+0w