Tue Nov 22 14:12:42 PST 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 Tue Nov 22 2011 at 14:12:46 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 0.6057512 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): -24.13700 34.63300 ymin,ymax (A): -20.25800 20.41200 zmin,zma (A): -2.690000 39.16800 x,y,z range (A): 58.77000 40.67000 41.85800 scale (grids/A): 0.6057512 object centre (A): 5.248002 7.6999664E-02 18.23900 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 292.6019 centred at (gu) : 89.87975 90.69106 90.22897 assigned negative charge : -287.6023 centred at (gu) : 89.89851 90.76929 90.34602 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4893 nv = 96 ne = 84 npr = 40194 no. pairs analyzed = 40194 no. exposed pairs = 2541 no. arc points = 17776 no. surface atoms = 854 nbur = 1112 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 242 mr = 2623 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2494 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1813 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 5891 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0194050E-09 -1.2896504E-09 midg,1,midg; midg,igrid,midg 4.3835859E-09 5.0224873E-11 1,midg,midg; igrid,midg,midg 3.3009508E-09 1.9529753E-09 gauss-seidel spectral radius is 0.9858391 estimated iterations to convergence 69 setup time was (sec) 0.4000000 now iterating at: 14:12:50 rms-change max change #iterations 0.1002608 21.15078 at 10iterations 8.5324440E-03 1.671632 at 20iterations 7.4241357E-04 0.1172870 at 30iterations 6.4063279E-05 9.7699165E-03 at 40iterations 5.4664324E-06 9.7846985E-04 at 50iterations finished qdiffx linear iterations at : 14:13:01 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 5.4664324E-06 9.7846985E-04 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 14:13:02 4.094u 0.244s 0:16.49 26.2% 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 Nov 22 2011 at 14:13:04 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 1.817254 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): -24.13700 34.63300 ymin,ymax (A): -20.25800 20.41200 zmin,zma (A): -2.690000 39.16800 x,y,z range (A): 58.77000 40.67000 41.85800 scale (grids/A): 1.817254 object centre (A): 5.248002 7.6999664E-02 18.23900 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 292.6019 centred at (gu) : 89.63893 92.07320 90.68708 assigned negative charge : -287.6023 centred at (gu) : 89.69568 92.30782 91.03835 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 52270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17776 grid for indexing accessible points = 1.400000 m= 18406 mr = 35364 m= 2488 mr = 13571 m= 111 mr = 1534 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 556 time to turn everything in is 0.2700000 number of dielectric boundary points 22788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 14346 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) : 0.6057512 object centre at (A) : 5.248002 7.6999664E-02 18.23900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0282379E-02 -1.8434615E-03 midg,1,midg; midg,igrid,midg 8.6769471E-03 3.0405652E-03 1,midg,midg; igrid,midg,midg 3.1376816E-02 1.7375259E-02 gauss-seidel spectral radius is 0.9984262 estimated iterations to convergence 200 setup time was (sec) 0.5500000 now iterating at: 14:13:09 rms-change max change #iterations 3.324887 157.8198 at 10iterations 1.465298 59.77996 at 20iterations 0.6492466 24.65770 at 30iterations 0.2866460 10.73497 at 40iterations 0.1268672 5.038229 at 50iterations 5.6144159E-02 2.068326 at 60iterations 2.4834130E-02 0.9256716 at 70iterations 1.0983279E-02 0.4310284 at 80iterations 4.8582768E-03 0.1827888 at 90iterations 2.1500695E-03 9.0640306E-02 at 100iterations 9.5168111E-04 3.5511971E-02 at 110iterations 4.2269466E-04 1.6989708E-02 at 120iterations finished qdiffx linear iterations at : 14:13:35 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 4.2269466E-04 1.6989708E-02 energy calculations done at 9.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.460000 DelPhi exited at 14:13:37 9.462u 0.302s 0:32.93 29.6% 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 Nov 22 2011 at 14:13:38 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 2.725880 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): -24.13700 34.63300 ymin,ymax (A): -20.25800 20.41200 zmin,zma (A): -2.690000 39.16800 x,y,z range (A): 58.77000 40.67000 41.85800 scale (grids/A): 2.725880 object centre (A): 5.248002 7.6999664E-02 18.23900 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 292.6019 centred at (gu) : 89.45837 93.10978 91.03059 assigned negative charge : -287.6023 centred at (gu) : 89.54359 93.46174 91.55754 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 120656 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17776 grid for indexing accessible points = 1.400000 m= 60172 mr = 85657 m= 21108 mr = 49232 m= 4369 mr = 17032 m= 464 mr = 3235 m= 24 mr = 281 m= 0 mr = 2 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1885 time to turn everything in is 0.7000000 number of dielectric boundary points 51354 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 14667 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) : 1.817254 object centre at (A) : 5.248002 7.6999664E-02 18.23900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5791200E-02 2.8058203E-04 midg,1,midg; midg,igrid,midg 7.8320719E-02 6.3854091E-02 1,midg,midg; igrid,midg,midg 0.3017415 0.1294555 gauss-seidel spectral radius is 0.9991835 estimated iterations to convergence 276 setup time was (sec) 0.9600000 now iterating at: 14:13:39 rms-change max change #iterations 7.959835 389.8287 at 10iterations 4.507073 115.0989 at 20iterations 2.537677 68.84895 at 30iterations 1.421841 35.44805 at 40iterations 0.7969052 17.34693 at 50iterations 0.4448147 9.336816 at 60iterations 0.2480694 5.608374 at 70iterations 0.1384414 2.799183 at 80iterations 7.7222630E-02 1.721920 at 90iterations 4.3206450E-02 0.9211578 at 100iterations 2.3990827E-02 0.5877838 at 110iterations 1.3414651E-02 0.2947311 at 120iterations 7.4730222E-03 0.1573224 at 130iterations 4.1600359E-03 9.5946789E-02 at 140iterations 2.3219311E-03 5.0684929E-02 at 150iterations 1.2929090E-03 3.1195953E-02 at 160iterations 7.2226516E-04 1.5095294E-02 at 170iterations 4.0214733E-04 8.9454651E-03 at 180iterations finished qdiffx linear iterations at : 14:14:16 total time elapsed so far: 13.71000 # loops : 180 mean,max change (kT/e) : 4.0214733E-04 8.9454651E-03 energy calculations done at 13.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.84000 DelPhi exited at 14:14:18 13.842u 0.275s 0:40.72 34.6% 0+0k 0+0io 0pf+0w