Tue Nov 22 14:10:42 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+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 Nov 22 2011 at 14:10:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 0.6245505 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): -35.22900 9.970000 ymin,ymax (A): 1.318000 42.45700 zmin,zma (A): -1.816000 55.18500 x,y,z range (A): 45.19900 41.13900 57.00100 scale (grids/A): 0.6245505 object centre (A): -12.62950 21.88750 26.68450 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 287.8221 centred at (gu) : 90.40619 89.22060 90.74976 assigned negative charge : -284.8223 centred at (gu) : 90.34667 89.35287 90.76936 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5216 nv = 96 ne = 84 npr = 40015 no. pairs analyzed = 40015 no. exposed pairs = 2471 no. arc points = 16911 no. surface atoms = 839 nbur = 1121 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 293 mr = 2898 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1688 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 6167 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2318919E-09 1.8804276E-09 midg,1,midg; midg,igrid,midg 1.1819215E-08 -3.9776080E-09 1,midg,midg; igrid,midg,midg -5.5814925E-10 6.5475869E-09 gauss-seidel spectral radius is 0.9866670 estimated iterations to convergence 71 setup time was (sec) 0.4300000 now iterating at: 14:10:50 rms-change max change #iterations 0.1108837 17.09947 at 10iterations 1.0186160E-02 1.915049 at 20iterations 9.5559197E-04 0.1701393 at 30iterations 8.6697415E-05 1.6105652E-02 at 40iterations 8.2242586E-06 1.2855530E-03 at 50iterations finished qdiffx linear iterations at : 14:10:58 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 8.2242586E-06 1.2855530E-03 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 14:11:02 3.187u 0.187s 0:16.09 20.8% 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 14:11:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 1.873651 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): -35.22900 9.970000 ymin,ymax (A): 1.318000 42.45700 zmin,zma (A): -1.816000 55.18500 x,y,z range (A): 45.19900 41.13900 57.00100 scale (grids/A): 1.873651 object centre (A): -12.62950 21.88750 26.68450 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 287.8221 centred at (gu) : 91.21846 87.66190 92.24956 assigned negative charge : -284.8223 centred at (gu) : 91.04021 88.05885 92.30831 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 55801 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16911 grid for indexing accessible points = 1.400000 m= 21021 mr = 38416 m= 3507 mr = 15999 m= 197 mr = 2422 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 378 time to turn everything in is 0.4100000 number of dielectric boundary points 23618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 14330 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) : 0.6245505 object centre at (A) : -12.62950 21.88750 26.68450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5375612E-02 3.6165405E-02 midg,1,midg; midg,igrid,midg 5.1118056E-03 -7.7832504E-03 1,midg,midg; igrid,midg,midg -2.8412289E-03 -1.9272312E-03 gauss-seidel spectral radius is 0.9985147 estimated iterations to convergence 206 setup time was (sec) 0.7100000 now iterating at: 14:11:09 rms-change max change #iterations 3.428028 153.7652 at 10iterations 1.552780 56.58189 at 20iterations 0.7036046 25.71955 at 30iterations 0.3195120 12.33187 at 40iterations 0.1448587 5.489936 at 50iterations 6.5482095E-02 2.361869 at 60iterations 2.9697465E-02 1.096214 at 70iterations 1.3485952E-02 0.4758644 at 80iterations 6.0900715E-03 0.2089789 at 90iterations 2.7648180E-03 0.1041603 at 100iterations 1.2540775E-03 4.7729015E-02 at 110iterations 5.6775083E-04 2.0268917E-02 at 120iterations finished qdiffx linear iterations at : 14:11:23 total time elapsed so far: 7.000000 # loops : 120 mean,max change (kT/e) : 5.6775083E-04 2.0268917E-02 energy calculations done at 7.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.180000 DelPhi exited at 14:11:25 7.178u 0.186s 0:21.32 34.4% 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 Tue Nov 22 2011 at 14:11:29 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 = 1960 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: 2.810477 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): -35.22900 9.970000 ymin,ymax (A): 1.318000 42.45700 zmin,zma (A): -1.816000 55.18500 x,y,z range (A): 45.19900 41.13900 57.00100 scale (grids/A): 2.810477 object centre (A): -12.62950 21.88750 26.68450 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000004 assigned positive charge : 287.8221 centred at (gu) : 91.82763 86.49284 93.37422 assigned negative charge : -284.8223 centred at (gu) : 91.56042 87.08817 93.46246 start vw surface at 0.1200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 128713 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16911 grid for indexing accessible points = 1.400000 m= 67271 mr = 92815 m= 25591 mr = 55811 m= 6287 mr = 21352 m= 877 mr = 5026 m= 65 mr = 642 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 1411 time to turn everything in is 1.030000 number of dielectric boundary points 53130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 14624 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) : 1.873651 object centre at (A) : -12.62950 21.88750 26.68450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9450382E-02 0.2425910 midg,1,midg; midg,igrid,midg -1.8690651E-02 -9.5646985E-02 1,midg,midg; igrid,midg,midg -6.3618779E-02 -4.7493089E-02 gauss-seidel spectral radius is 0.9992090 estimated iterations to convergence 281 setup time was (sec) 1.340000 now iterating at: 14:11:34 rms-change max change #iterations 8.126045 300.7237 at 10iterations 4.652750 152.4674 at 20iterations 2.629864 59.19729 at 30iterations 1.496307 31.64869 at 40iterations 0.8439881 18.02951 at 50iterations 0.4758025 11.40714 at 60iterations 0.2679622 5.707338 at 70iterations 0.1511724 2.991174 at 80iterations 8.5110389E-02 1.682872 at 90iterations 4.7915999E-02 0.9427977 at 100iterations 2.6981482E-02 0.5819473 at 110iterations 1.5173730E-02 0.2962275 at 120iterations 8.5412636E-03 0.1792526 at 130iterations 4.8063067E-03 0.1022515 at 140iterations 2.7013046E-03 6.5479964E-02 at 150iterations 1.5217796E-03 3.1214714E-02 at 160iterations 8.5568835E-04 1.7149687E-02 at 170iterations 4.8064018E-04 1.1061668E-02 at 180iterations finished qdiffx linear iterations at : 14:12:01 total time elapsed so far: 11.38000 # loops : 180 mean,max change (kT/e) : 4.8064018E-04 1.1061668E-02 energy calculations done at 11.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.55000 DelPhi exited at 14:12:02 11.551u 0.223s 0:33.81 34.8% 0+0k 0+0io 0pf+0w