Mon Oct 10 09:16:26 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 09:16:26 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.5781192 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): -26.20000 35.37900 ymin,ymax (A): -19.14200 20.42400 zmin,zma (A): -3.180000 38.88400 x,y,z range (A): 61.57900 39.56600 42.06400 scale (grids/A): 0.5781192 object centre (A): 4.589501 0.6409998 17.85200 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 90.22601 90.32876 90.40372 assigned negative charge : -288.0262 centred at (gu) : 90.22988 90.40034 90.51035 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4346 nv = 96 ne = 84 npr = 40439 no. pairs analyzed = 40439 no. exposed pairs = 2414 no. arc points = 17059 no. surface atoms = 813 nbur = 1151 mkacc time = 6.9999993E-02 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 = 1.512000 m= 185 mr = 2359 m= 0 mr = 9 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.1700000 number of dielectric boundary points 2163 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1812 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5507 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8524131E-09 -9.0914631E-10 midg,1,midg; midg,igrid,midg 1.4600060E-09 -3.7298048E-10 1,midg,midg; igrid,midg,midg 6.4331523E-10 6.0364780E-10 gauss-seidel spectral radius is 0.9844735 estimated iterations to convergence 66 setup time was (sec) 0.3600000 now iterating at: 09:16:26 rms-change max change #iterations 8.1193641E-02 15.06647 at 10iterations 6.0536419E-03 1.041143 at 20iterations 4.7566401E-04 9.0819836E-02 at 30iterations 3.6477428E-05 5.9518814E-03 at 40iterations 2.8257239E-06 5.0258636E-04 at 50iterations finished qdiffx linear iterations at : 09:16:29 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.8257239E-06 5.0258636E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 09:16:30 3.375u 0.164s 0:03.82 92.4% 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 09:16:30 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.734357 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): -26.20000 35.37900 ymin,ymax (A): -19.14200 20.42400 zmin,zma (A): -3.180000 38.88400 x,y,z range (A): 61.57900 39.56600 42.06400 scale (grids/A): 1.734357 object centre (A): 4.589501 0.6409998 17.85200 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 90.67789 90.98618 91.21095 assigned negative charge : -288.0262 centred at (gu) : 90.68970 91.20117 91.53093 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 47848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17059 grid for indexing accessible points = 1.400000 m= 16255 mr = 32720 m= 1730 mr = 12182 m= 41 mr = 962 m= 0 mr = 10 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 571 time to turn everything in is 0.2500000 number of dielectric boundary points 20000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 14171 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) : 0.5781192 object centre at (A) : 4.589501 0.6409998 17.85200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2815184E-03 -4.9098907E-03 midg,1,midg; midg,igrid,midg 2.1613555E-03 -1.6330521E-03 1,midg,midg; igrid,midg,midg 3.0085849E-02 3.1809252E-02 gauss-seidel spectral radius is 0.9982766 estimated iterations to convergence 191 setup time was (sec) 0.4600000 now iterating at: 09:16:30 rms-change max change #iterations 3.026927 180.4100 at 10iterations 1.284744 56.06648 at 20iterations 0.5476496 24.30002 at 30iterations 0.2342851 10.02870 at 40iterations 9.9555917E-02 3.957217 at 50iterations 4.2585757E-02 1.677573 at 60iterations 1.8141702E-02 0.7886505 at 70iterations 7.7093355E-03 0.3140879 at 80iterations 3.3092857E-03 0.1454983 at 90iterations 1.4040974E-03 5.5402756E-02 at 100iterations 5.9966830E-04 2.3880005E-02 at 110iterations 2.5489458E-04 1.0476112E-02 at 120iterations finished qdiffx linear iterations at : 09:16:37 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 2.5489458E-04 1.0476112E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 09:16:38 7.548u 0.189s 0:08.04 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 Mon Oct 10 2011 at 09:16:38 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.601536 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): -26.20000 35.37900 ymin,ymax (A): -19.14200 20.42400 zmin,zma (A): -3.180000 38.88400 x,y,z range (A): 61.57900 39.56600 42.06400 scale (grids/A): 2.601536 object centre (A): 4.589501 0.6409998 17.85200 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 91.01691 91.47930 91.81652 assigned negative charge : -288.0262 centred at (gu) : 91.03471 91.80177 92.29644 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 110702 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17059 grid for indexing accessible points = 1.400000 m= 54345 mr = 79265 m= 17397 mr = 44718 m= 2844 mr = 14210 m= 203 mr = 2045 m= 5 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 2092 time to turn everything in is 0.5800000 number of dielectric boundary points 45131 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 14648 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) : 1.734357 object centre at (A) : 4.589501 0.6409998 17.85200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3973650E-02 -5.1969882E-02 midg,1,midg; midg,igrid,midg 1.4429274E-02 -1.6161760E-02 1,midg,midg; igrid,midg,midg 0.4057453 0.3911328 gauss-seidel spectral radius is 0.9991344 estimated iterations to convergence 269 setup time was (sec) 0.8000000 now iterating at: 09:16:39 rms-change max change #iterations 7.420734 260.1577 at 10iterations 4.095809 117.0737 at 20iterations 2.254114 53.34570 at 30iterations 1.239270 32.55077 at 40iterations 0.6812718 15.52542 at 50iterations 0.3721478 8.242220 at 60iterations 0.2043729 4.529537 at 70iterations 0.1118715 2.399819 at 80iterations 6.1474338E-02 1.394924 at 90iterations 3.3516217E-02 0.7972088 at 100iterations 1.8305628E-02 0.4062881 at 110iterations 1.0022665E-02 0.2292137 at 120iterations 5.4941531E-03 0.1449509 at 130iterations 3.0025116E-03 7.3040009E-02 at 140iterations 1.6448324E-03 3.7429810E-02 at 150iterations 9.0192171E-04 1.9540548E-02 at 160iterations 4.9343461E-04 1.1352539E-02 at 170iterations 2.7006314E-04 6.2637329E-03 at 180iterations finished qdiffx linear iterations at : 09:16:49 total time elapsed so far: 11.54000 # loops : 180 mean,max change (kT/e) : 2.7006314E-04 6.2637329E-03 energy calculations done at 11.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.68000 DelPhi exited at 09:16:50 11.681u 0.203s 0:12.16 97.6% 0+0k 0+0io 0pf+0w