Mon Oct 10 14:38:56 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 Mon Oct 10 2011 at 14:38:56 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6555203 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): 17.53300 71.84100 ymin,ymax (A): 26.51700 72.64700 zmin,zma (A): 28.27900 78.61500 x,y,z range (A): 54.30800 46.13000 50.33600 scale (grids/A): 0.6555203 object centre (A): 44.68700 49.58200 53.44700 number of atom coordinates read : 2364 total number of charged atoms : 2231 net assigned charge : -3.499990 assigned positive charge : 358.1852 centred at (gu) : 90.29845 89.31984 90.28010 assigned negative charge : -361.6858 centred at (gu) : 90.11021 89.33334 90.35105 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6887 nv = 96 ne = 84 npr = 48813 no. pairs analyzed = 48813 no. exposed pairs = 3000 no. arc points = 20972 no. surface atoms = 1026 nbur = 1338 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 413 mr = 3761 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3486 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2029 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8103 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4099996E-09 -2.0854339E-08 midg,1,midg; midg,igrid,midg -6.5296772E-09 -8.8310106E-09 1,midg,midg; igrid,midg,midg -3.7062751E-08 2.3890987E-08 gauss-seidel spectral radius is 0.9879221 estimated iterations to convergence 74 setup time was (sec) 0.5300000 now iterating at: 14:38:57 rms-change max change #iterations 0.1576032 30.74529 at 10iterations 1.6321257E-02 2.083923 at 20iterations 1.7867591E-03 0.2692738 at 30iterations 2.6779503E-04 3.7704468E-02 at 40iterations 6.6128363E-05 1.0606766E-02 at 50iterations finished qdiffx linear iterations at : 14:38:59 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 6.6128363E-05 1.0606766E-02 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 14:39:00 3.264u 0.186s 0:03.95 87.0% 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 Mon Oct 10 2011 at 14:39:00 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.966561 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): 17.53300 71.84100 ymin,ymax (A): 26.51700 72.64700 zmin,zma (A): 28.27900 78.61500 x,y,z range (A): 54.30800 46.13000 50.33600 scale (grids/A): 1.966561 object centre (A): 44.68700 49.58200 53.44700 number of atom coordinates read : 2364 total number of charged atoms : 2231 net assigned charge : -3.499990 assigned positive charge : 358.1852 centred at (gu) : 90.89488 87.95903 90.84001 assigned negative charge : -361.6858 centred at (gu) : 90.33051 87.99992 91.05301 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 74005 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20972 grid for indexing accessible points = 1.400000 m= 27735 mr = 51190 m= 4984 mr = 20462 m= 383 mr = 3133 m= 2 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 32184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 17638 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) : 0.6555203 object centre at (A) : 44.68700 49.58200 53.44700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7054187E-02 -3.5954356E-02 midg,1,midg; midg,igrid,midg -1.8477289E-03 -1.1046479E-02 1,midg,midg; igrid,midg,midg -8.4584588E-03 3.0280249E-02 gauss-seidel spectral radius is 0.9987003 estimated iterations to convergence 220 setup time was (sec) 0.8700000 now iterating at: 14:39:01 rms-change max change #iterations 4.405152 231.2975 at 10iterations 2.101988 88.05772 at 20iterations 0.9971877 35.19741 at 30iterations 0.4775335 14.65524 at 40iterations 0.2273753 7.125060 at 50iterations 0.1086797 3.690770 at 60iterations 5.2003637E-02 1.609859 at 70iterations 2.4786910E-02 0.7350655 at 80iterations 1.1848017E-02 0.3670044 at 90iterations 5.6711631E-03 0.1821479 at 100iterations 2.7391596E-03 9.8907471E-02 at 110iterations 1.3359411E-03 4.1587830E-02 at 120iterations finished qdiffx linear iterations at : 14:39:08 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 1.3359411E-03 4.1587830E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 14:39:08 7.519u 0.216s 0:08.05 95.9% 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 Mon Oct 10 2011 at 14:39:08 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.949841 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): 17.53300 71.84100 ymin,ymax (A): 26.51700 72.64700 zmin,zma (A): 28.27900 78.61500 x,y,z range (A): 54.30800 46.13000 50.33600 scale (grids/A): 2.949841 object centre (A): 44.68700 49.58200 53.44700 number of atom coordinates read : 2364 total number of charged atoms : 2231 net assigned charge : -3.499990 assigned positive charge : 358.1852 centred at (gu) : 91.34209 86.93844 91.26003 assigned negative charge : -361.6858 centred at (gu) : 90.49582 86.99988 91.57936 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 171125 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20972 grid for indexing accessible points = 1.400000 m= 87595 mr = 123870 m= 34040 mr = 71698 m= 9136 mr = 27306 m= 1544 mr = 6859 m= 113 mr = 1030 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.370000 number of dielectric boundary points 72758 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 17844 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) : 1.966561 object centre at (A) : 44.68700 49.58200 53.44700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3800134 -0.2284534 midg,1,midg; midg,igrid,midg 6.5133020E-02 -5.3566299E-02 1,midg,midg; igrid,midg,midg -5.0690374E-03 0.3381432 gauss-seidel spectral radius is 0.9992695 estimated iterations to convergence 292 setup time was (sec) 1.710000 now iterating at: 14:39:10 rms-change max change #iterations 10.15533 360.9128 at 10iterations 5.971751 140.7487 at 20iterations 3.497832 76.67208 at 30iterations 2.042262 43.08311 at 40iterations 1.189556 23.26803 at 50iterations 0.6916918 12.74071 at 60iterations 0.4012980 7.482209 at 70iterations 0.2328268 4.184107 at 80iterations 0.1350346 3.098353 at 90iterations 7.8048512E-02 1.502887 at 100iterations 4.5162350E-02 0.7516599 at 110iterations 2.6141563E-02 0.5151958 at 120iterations 1.5094073E-02 0.3158455 at 130iterations 8.7215155E-03 0.1658096 at 140iterations 5.0584017E-03 9.1391563E-02 at 150iterations 2.9264556E-03 5.7737350E-02 at 160iterations 1.7041488E-03 3.1097412E-02 at 170iterations 9.9948479E-04 1.8312454E-02 at 180iterations finished qdiffx linear iterations at : 14:39:21 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 9.9948479E-04 1.8312454E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 14:39:21 12.694u 0.241s 0:13.23 97.7% 0+0k 0+0io 0pf+0w