Sun Oct 9 15:04:20 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 Sun Oct 9 2011 at 15:04:20 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 = 2927 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: 0.5633357 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): 0.8360001 49.32900 ymin,ymax (A): -17.14500 31.50400 zmin,zma (A): 124.5990 187.7940 x,y,z range (A): 48.49300 48.64900 63.19501 scale (grids/A): 0.5633357 object centre (A): 25.08250 7.179500 156.1965 number of atom coordinates read : 2927 total number of charged atoms : 2786 net assigned charge : 8.500023 assigned positive charge : 436.5444 centred at (gu) : 90.60550 89.50768 89.20452 assigned negative charge : -428.0454 centred at (gu) : 90.60586 89.55843 89.25668 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6297 nv = 96 ne = 84 npr = 57226 no. pairs analyzed = 57226 no. exposed pairs = 3873 no. arc points = 27507 no. surface atoms = 1280 nbur = 1647 mkacc time = 0.1000000 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 = 1.540000 m= 262 mr = 3223 m= 1 mr = 9 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 3328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2840 ## 344 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8030 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9769129E-09 3.2393177E-10 midg,1,midg; midg,igrid,midg 1.8198109E-09 3.6058398E-10 1,midg,midg; igrid,midg,midg 8.8423441E-10 1.1625122E-09 gauss-seidel spectral radius is 0.9837475 estimated iterations to convergence 65 setup time was (sec) 0.4100000 now iterating at: 15:04:20 rms-change max change #iterations 8.3334491E-02 14.46904 at 10iterations 6.0771601E-03 0.9038887 at 20iterations 4.3804199E-04 6.1745644E-02 at 30iterations 3.3461576E-05 4.8103333E-03 at 40iterations 2.9312771E-06 3.9100647E-04 at 50iterations finished qdiffx linear iterations at : 15:04:23 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 2.9312771E-06 3.9100647E-04 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 15:04:24 3.452u 0.174s 0:03.98 90.9% 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 Sun Oct 9 2011 at 15:04:24 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 = 2927 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: 1.690007 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): 0.8360001 49.32900 ymin,ymax (A): -17.14500 31.50400 zmin,zma (A): 124.5990 187.7940 x,y,z range (A): 48.49300 48.64900 63.19501 scale (grids/A): 1.690007 object centre (A): 25.08250 7.179500 156.1965 number of atom coordinates read : 2927 total number of charged atoms : 2786 net assigned charge : 8.500023 assigned positive charge : 436.5444 centred at (gu) : 91.81592 88.52234 87.61291 assigned negative charge : -428.0454 centred at (gu) : 91.81736 88.67516 87.76979 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 68741 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27507 grid for indexing accessible points = 1.400000 m= 22179 mr = 45879 m= 2580 mr = 15394 m= 80 mr = 1341 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 99 time to turn everything in is 0.3400000 number of dielectric boundary points 30957 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 307 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 21507 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) : 0.5633357 object centre at (A) : 25.08250 7.179500 156.1965 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8367442E-03 1.5915046E-02 midg,1,midg; midg,igrid,midg 4.2989571E-03 -1.0165144E-03 1,midg,midg; igrid,midg,midg 9.5391562E-03 1.2730914E-02 gauss-seidel spectral radius is 0.9983117 estimated iterations to convergence 193 setup time was (sec) 0.5500000 now iterating at: 15:04:24 rms-change max change #iterations 3.496034 153.1421 at 10iterations 1.500097 76.07855 at 20iterations 0.6450897 22.14043 at 30iterations 0.2766310 9.724884 at 40iterations 0.1189418 4.246113 at 50iterations 5.1140539E-02 1.945685 at 60iterations 2.1904485E-02 0.7876225 at 70iterations 9.4575472E-03 0.3415127 at 80iterations 4.0710857E-03 0.1570616 at 90iterations 1.7443204E-03 6.1788201E-02 at 100iterations 7.5403386E-04 2.6591301E-02 at 110iterations 3.2376827E-04 1.1683464E-02 at 120iterations finished qdiffx linear iterations at : 15:04:32 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 3.2376827E-04 1.1683464E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 15:04:32 7.865u 0.209s 0:08.50 94.8% 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 Sun Oct 9 2011 at 15:04:32 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 = 2927 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: 2.535010 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): 0.8360001 49.32900 ymin,ymax (A): -17.14500 31.50400 zmin,zma (A): 124.5990 187.7940 x,y,z range (A): 48.49300 48.64900 63.19501 scale (grids/A): 2.535010 object centre (A): 25.08250 7.179500 156.1965 number of atom coordinates read : 2927 total number of charged atoms : 2786 net assigned charge : 8.500023 assigned positive charge : 436.5444 centred at (gu) : 92.72379 87.78328 86.41911 assigned negative charge : -428.0454 centred at (gu) : 92.72569 88.01273 86.65466 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 159272 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27507 grid for indexing accessible points = 1.400000 m= 75353 mr = 112350 m= 23098 mr = 59554 m= 4135 mr = 17519 m= 327 mr = 2779 m= 9 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 358 time to turn everything in is 0.8200000 number of dielectric boundary points 69851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 22275 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) : 1.690007 object centre at (A) : 25.08250 7.179500 156.1965 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1890535 0.1105551 midg,1,midg; midg,igrid,midg 4.2729914E-02 -2.8728424E-02 1,midg,midg; igrid,midg,midg 0.1337542 0.1715222 gauss-seidel spectral radius is 0.9991769 estimated iterations to convergence 275 setup time was (sec) 1.050000 now iterating at: 15:04:33 rms-change max change #iterations 8.925524 271.5067 at 10iterations 5.114176 136.4422 at 20iterations 2.895305 60.20670 at 30iterations 1.640057 34.02701 at 40iterations 0.9209062 21.51743 at 50iterations 0.5174724 11.19660 at 60iterations 0.2895553 6.726473 at 70iterations 0.1620598 3.552464 at 80iterations 9.0677187E-02 1.807541 at 90iterations 5.0555862E-02 0.9907191 at 100iterations 2.8175727E-02 0.5688415 at 110iterations 1.5711354E-02 0.3127031 at 120iterations 8.7601766E-03 0.1802139 at 130iterations 4.8808311E-03 0.1101589 at 140iterations 2.7258240E-03 5.4985046E-02 at 150iterations 1.5145796E-03 3.2882690E-02 at 160iterations 8.4475154E-04 1.6052246E-02 at 170iterations 4.6828162E-04 1.0409355E-02 at 180iterations finished qdiffx linear iterations at : 15:04:45 total time elapsed so far: 12.39000 # loops : 180 mean,max change (kT/e) : 4.6828162E-04 1.0409355E-02 energy calculations done at 12.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.52000 DelPhi exited at 15:04:45 12.526u 0.213s 0:13.02 97.7% 0+0k 0+0io 0pf+0w