Wed Dec 28 11:03:06 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+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 Wed Dec 28 2011 at 11:03:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 0.6448341 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): -6.128000 35.09600 ymin,ymax (A): -3.976000 49.75300 zmin,zma (A): -24.32800 30.88000 x,y,z range (A): 41.22400 53.72900 55.20800 scale (grids/A): 0.6448341 object centre (A): 14.48400 22.88850 3.276001 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 287.8261 centred at (gu) : 90.83497 92.49645 90.21099 assigned negative charge : -283.8263 centred at (gu) : 90.92544 92.60960 90.14748 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5621 nv = 96 ne = 84 npr = 40206 no. pairs analyzed = 40206 no. exposed pairs = 2359 no. arc points = 16824 no. surface atoms = 807 nbur = 1155 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 282 mr = 3193 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 91 time to turn everything in is 0.3100000 number of dielectric boundary points 2662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1719 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 6610 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3363660E-10 1.3696562E-08 midg,1,midg; midg,igrid,midg 1.0557812E-08 -7.3196551E-09 1,midg,midg; igrid,midg,midg 1.3130591E-08 -2.2221052E-09 gauss-seidel spectral radius is 0.9874820 estimated iterations to convergence 73 setup time was (sec) 0.7900000 now iterating at: 11:03:07 rms-change max change #iterations 0.1253939 19.71792 at 10iterations 1.2811379E-02 1.970507 at 20iterations 1.3025301E-03 0.2588429 at 30iterations 1.2848385E-04 2.1184921E-02 at 40iterations 1.2891010E-05 1.8348694E-03 at 50iterations finished qdiffx linear iterations at : 11:03:13 total time elapsed so far: 6.890000 # loops : 50 mean,max change (kT/e) : 1.2891010E-05 1.8348694E-03 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 11:03:14 7.055u 0.605s 0:08.10 94.4% 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 Wed Dec 28 2011 at 11:03:14 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 = 1962 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: 1.934502 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): -6.128000 35.09600 ymin,ymax (A): -3.976000 49.75300 zmin,zma (A): -24.32800 30.88000 x,y,z range (A): 41.22400 53.72900 55.20800 scale (grids/A): 1.934502 object centre (A): 14.48400 22.88850 3.276001 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 287.8261 centred at (gu) : 92.50485 97.48924 90.63296 assigned negative charge : -283.8263 centred at (gu) : 92.77660 97.82896 90.44250 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 60584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16824 grid for indexing accessible points = 1.400000 m= 23094 mr = 42482 m= 3564 mr = 17997 m= 211 mr = 2328 m= 7 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2898 time to turn everything in is 0.6200000 number of dielectric boundary points 24559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 104 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 14434 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) : 0.6448341 object centre at (A) : 14.48400 22.88850 3.276001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2935655E-02 2.1791222E-02 midg,1,midg; midg,igrid,midg 2.7534248E-02 -4.2046099E-03 1,midg,midg; igrid,midg,midg 9.9754538E-03 -1.6001730E-03 gauss-seidel spectral radius is 0.9985971 estimated iterations to convergence 212 setup time was (sec) 1.170000 now iterating at: 11:03:16 rms-change max change #iterations 3.659872 199.8202 at 10iterations 1.704780 63.80647 at 20iterations 0.7892425 30.60785 at 30iterations 0.3672175 13.51737 at 40iterations 0.1695553 6.275009 at 50iterations 7.8235142E-02 2.931519 at 60iterations 3.6421049E-02 1.411243 at 70iterations 1.6844278E-02 0.5692387 at 80iterations 7.8129312E-03 0.3300438 at 90iterations 3.6295776E-03 0.1314735 at 100iterations 1.6805925E-03 5.9965968E-02 at 110iterations 7.7914284E-04 2.5653839E-02 at 120iterations finished qdiffx linear iterations at : 11:03:33 total time elapsed so far: 18.36000 # loops : 120 mean,max change (kT/e) : 7.7914284E-04 2.5653839E-02 energy calculations done at 18.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.52000 DelPhi exited at 11:03:34 18.526u 0.822s 0:19.73 98.0% 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 Wed Dec 28 2011 at 11:03:34 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 = 1962 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: 2.901753 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): -6.128000 35.09600 ymin,ymax (A): -3.976000 49.75300 zmin,zma (A): -24.32800 30.88000 x,y,z range (A): 41.22400 53.72900 55.20800 scale (grids/A): 2.901753 object centre (A): 14.48400 22.88850 3.276001 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 287.8261 centred at (gu) : 93.75732 101.2338 90.94942 assigned negative charge : -283.8263 centred at (gu) : 94.16502 101.7435 90.66388 start vw surface at 0.1100000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 140033 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16824 grid for indexing accessible points = 1.400000 m= 74179 mr = 102526 m= 27754 mr = 62469 m= 6351 mr = 23230 m= 886 mr = 4946 m= 58 mr = 583 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 10407 time to turn everything in is 1.440000 number of dielectric boundary points 55483 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 14640 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) : 1.934502 object centre at (A) : 14.48400 22.88850 3.276001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.021221 7.5003222E-02 midg,1,midg; midg,igrid,midg 0.2426607 -8.0647670E-02 1,midg,midg; igrid,midg,midg 6.0159199E-02 -6.1153453E-03 gauss-seidel spectral radius is 0.9992346 estimated iterations to convergence 285 setup time was (sec) 2.040000 now iterating at: 11:03:37 rms-change max change #iterations 8.517529 387.4043 at 10iterations 4.869992 120.0573 at 20iterations 2.774732 70.77028 at 30iterations 1.577774 32.27174 at 40iterations 0.8958128 18.67971 at 50iterations 0.5100545 11.04669 at 60iterations 0.2886422 5.910405 at 70iterations 0.1640523 3.585451 at 80iterations 9.3274951E-02 1.928945 at 90iterations 5.2931834E-02 1.055337 at 100iterations 3.0062864E-02 0.6606116 at 110iterations 1.7048515E-02 0.3396378 at 120iterations 9.6868305E-03 0.1836960 at 130iterations 5.5000721E-03 0.1146851 at 140iterations 3.1202775E-03 5.7682037E-02 at 150iterations 1.7768319E-03 3.6869049E-02 at 160iterations 1.0057965E-03 2.1255493E-02 at 170iterations 5.7254062E-04 1.0124207E-02 at 180iterations finished qdiffx linear iterations at : 11:04:06 total time elapsed so far: 31.09000 # loops : 180 mean,max change (kT/e) : 5.7254062E-04 1.0124207E-02 energy calculations done at 31.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 31.27000 DelPhi exited at 11:04:07 31.277u 0.728s 0:32.60 98.1% 0+0k 0+0io 0pf+0w