Tue Oct 11 07:50:36 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 Tue Oct 11 2011 at 07:50:37 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 = 2381 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6365440 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): -8.921000 36.58800 ymin,ymax (A): -14.92200 41.00500 zmin,zma (A): 5.279000 52.25400 x,y,z range (A): 45.50900 55.92700 46.97500 scale (grids/A): 0.6365440 object centre (A): 13.83350 13.04150 28.76650 number of atom coordinates read : 2381 total number of charged atoms : 2245 net assigned charge : 4.500007 assigned positive charge : 357.2813 centred at (gu) : 90.42207 88.75338 90.74741 assigned negative charge : -352.7818 centred at (gu) : 90.34354 88.75636 90.89935 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6477 nv = 96 ne = 84 npr = 47983 no. pairs analyzed = 47983 no. exposed pairs = 2903 no. arc points = 20299 no. surface atoms = 989 nbur = 1392 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 382 mr = 3599 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2115 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7370727E-08 -1.0504747E-08 midg,1,midg; midg,igrid,midg 8.1854239E-09 4.4321382E-09 1,midg,midg; igrid,midg,midg -1.4398904E-09 1.4789136E-08 gauss-seidel spectral radius is 0.9871933 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 07:50:37 rms-change max change #iterations 0.1360576 20.47809 at 10iterations 1.3498819E-02 1.958549 at 20iterations 1.6015712E-03 0.2307873 at 30iterations 2.8716936E-04 4.3313980E-02 at 40iterations 7.0980619E-05 1.0791779E-02 at 50iterations finished qdiffx linear iterations at : 07:50:41 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 7.0980619E-05 1.0791779E-02 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 07:50:42 4.414u 0.386s 0:05.58 85.8% 0+0k 0+0io 4pf+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 Oct 11 2011 at 07:50:42 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 = 2381 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: 1.909632 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): -8.921000 36.58800 ymin,ymax (A): -14.92200 41.00500 zmin,zma (A): 5.279000 52.25400 x,y,z range (A): 45.50900 55.92700 46.97500 scale (grids/A): 1.909632 object centre (A): 13.83350 13.04150 28.76650 number of atom coordinates read : 2381 total number of charged atoms : 2245 net assigned charge : 4.500007 assigned positive charge : 357.2813 centred at (gu) : 91.26575 86.25960 92.24169 assigned negative charge : -352.7818 centred at (gu) : 91.03056 86.26908 92.69785 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20299 grid for indexing accessible points = 1.400000 m= 26514 mr = 48091 m= 4336 mr = 19783 m= 275 mr = 2680 m= 5 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 29585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 17637 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) : 0.6365440 object centre at (A) : 13.83350 13.04150 28.76650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5545334E-02 -2.1351075E-02 midg,1,midg; midg,igrid,midg 1.5283493E-02 3.1500798E-02 1,midg,midg; igrid,midg,midg -3.4049598E-03 7.8446474E-03 gauss-seidel spectral radius is 0.9986200 estimated iterations to convergence 213 setup time was (sec) 0.8900000 now iterating at: 07:50:43 rms-change max change #iterations 3.994277 187.7469 at 10iterations 1.862647 69.47940 at 20iterations 0.8762860 28.13492 at 30iterations 0.4072489 12.60285 at 40iterations 0.1911491 6.244503 at 50iterations 8.9246586E-02 3.059502 at 60iterations 4.1666690E-02 1.391335 at 70iterations 1.9554952E-02 0.6184621 at 80iterations 9.1942968E-03 0.3227806 at 90iterations 4.3805311E-03 0.1564827 at 100iterations 2.1027266E-03 6.9698334E-02 at 110iterations 1.0314137E-03 3.5335541E-02 at 120iterations finished qdiffx linear iterations at : 07:50:53 total time elapsed so far: 10.36000 # loops : 120 mean,max change (kT/e) : 1.0314137E-03 3.5335541E-02 energy calculations done at 10.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.52000 DelPhi exited at 07:50:54 10.525u 0.435s 0:11.52 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 Tue Oct 11 2011 at 07:50:54 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 = 2381 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.864448 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): -8.921000 36.58800 ymin,ymax (A): -14.92200 41.00500 zmin,zma (A): 5.279000 52.25400 x,y,z range (A): 45.50900 55.92700 46.97500 scale (grids/A): 2.864448 object centre (A): 13.83350 13.04150 28.76650 number of atom coordinates read : 2381 total number of charged atoms : 2245 net assigned charge : 4.500007 assigned positive charge : 357.2813 centred at (gu) : 91.89850 84.38923 93.36244 assigned negative charge : -352.7818 centred at (gu) : 91.54572 84.40359 94.04675 start vw surface at 0.1200000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 159454 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20299 grid for indexing accessible points = 1.400000 m= 84224 mr = 116212 m= 31778 mr = 69236 m= 7609 mr = 25787 m= 1084 mr = 5571 m= 102 mr = 755 m= 0 mr = 48 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.550000 number of dielectric boundary points 66642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 17956 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) : 1.909632 object centre at (A) : 13.83350 13.04150 28.76650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4007234 -0.3074743 midg,1,midg; midg,igrid,midg 7.2852246E-02 0.3144692 1,midg,midg; igrid,midg,midg -1.8404679E-02 -7.7545142E-04 gauss-seidel spectral radius is 0.9992471 estimated iterations to convergence 288 setup time was (sec) 1.880000 now iterating at: 07:50:56 rms-change max change #iterations 9.545608 331.2409 at 10iterations 5.586002 129.4034 at 20iterations 3.246310 72.93030 at 30iterations 1.882917 40.57379 at 40iterations 1.087540 21.37341 at 50iterations 0.6262544 12.60089 at 60iterations 0.3604356 6.811970 at 70iterations 0.2068785 3.956295 at 80iterations 0.1188139 2.490784 at 90iterations 6.8130262E-02 1.373461 at 100iterations 3.9143287E-02 0.7446804 at 110iterations 2.2433620E-02 0.4257603 at 120iterations 1.2859370E-02 0.2620430 at 130iterations 7.3708263E-03 0.1410370 at 140iterations 4.2326911E-03 7.6995492E-02 at 150iterations 2.4346896E-03 4.6907425E-02 at 160iterations 1.4126603E-03 2.5833130E-02 at 170iterations 8.2549220E-04 1.4794350E-02 at 180iterations finished qdiffx linear iterations at : 07:51:12 total time elapsed so far: 17.97000 # loops : 180 mean,max change (kT/e) : 8.2549220E-04 1.4794350E-02 energy calculations done at 17.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.14000 DelPhi exited at 07:51:13 18.141u 0.452s 0:19.24 96.6% 0+0k 0+0io 0pf+0w