Tue Oct 11 08:21:18 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+sph2.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 = amb2.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 08:21:18 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3105 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: 0.5744715 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): -23.80900 33.77500 ymin,ymax (A): -39.12600 22.84400 zmin,zma (A): -32.36500 29.41800 x,y,z range (A): 57.58400 61.97000 61.78300 scale (grids/A): 0.5744715 object centre (A): 4.983001 -8.141000 -1.473498 number of atom coordinates read : 3105 total number of charged atoms : 2952 net assigned charge : -2.999958 assigned positive charge : 457.5712 centred at (gu) : 90.13265 91.42600 92.42863 assigned negative charge : -460.5723 centred at (gu) : 90.22192 91.34155 92.55376 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6960 nv = 96 ne = 84 npr = 59745 no. pairs analyzed = 59745 no. exposed pairs = 4482 no. arc points = 31795 no. surface atoms = 1482 nbur = 1623 mkacc time = 0.1400000 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 = 1.484000 m= 303 mr = 3320 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3138 ## 335 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8787 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0171513E-09 -5.1740181E-09 midg,1,midg; midg,igrid,midg -1.4947984E-09 1.5358639E-09 1,midg,midg; igrid,midg,midg 1.1291915E-09 -2.2536344E-09 gauss-seidel spectral radius is 0.9843897 estimated iterations to convergence 66 setup time was (sec) 0.5700000 now iterating at: 08:21:19 rms-change max change #iterations 9.3162075E-02 17.08487 at 10iterations 7.0491522E-03 1.024647 at 20iterations 5.3456146E-04 8.2721710E-02 at 30iterations 4.0823128E-05 6.1931610E-03 at 40iterations 3.3325598E-06 5.2165985E-04 at 50iterations finished qdiffx linear iterations at : 08:21:21 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.3325598E-06 5.2165985E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 08:21:22 3.462u 0.178s 0:03.98 91.2% 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 08:21:22 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3105 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: 1.723415 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): -23.80900 33.77500 ymin,ymax (A): -39.12600 22.84400 zmin,zma (A): -32.36500 29.41800 x,y,z range (A): 57.58400 61.97000 61.78300 scale (grids/A): 1.723415 object centre (A): 4.983001 -8.141000 -1.473498 number of atom coordinates read : 3105 total number of charged atoms : 2952 net assigned charge : -2.999958 assigned positive charge : 457.5712 centred at (gu) : 90.39729 94.27742 97.28496 assigned negative charge : -460.5723 centred at (gu) : 90.66563 94.02439 97.66132 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 75846 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31795 grid for indexing accessible points = 1.400000 m= 23917 mr = 48752 m= 2691 mr = 16061 m= 84 mr = 1321 m= 0 mr = 17 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 36387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 265 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 22932 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) : 0.5744715 object centre at (A) : 4.983001 -8.141000 -1.473498 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9868416E-03 -3.9409820E-02 midg,1,midg; midg,igrid,midg -2.8502084E-02 -1.7949436E-02 1,midg,midg; igrid,midg,midg 1.1898887E-02 -8.9525767E-03 gauss-seidel spectral radius is 0.9984066 estimated iterations to convergence 199 setup time was (sec) 0.8800000 now iterating at: 08:21:23 rms-change max change #iterations 3.833601 174.8670 at 10iterations 1.669840 61.91817 at 20iterations 0.7347106 23.94257 at 30iterations 0.3221186 10.54494 at 40iterations 0.1419669 4.543209 at 50iterations 6.2210463E-02 2.017439 at 60iterations 2.7412275E-02 0.8386641 at 70iterations 1.2055076E-02 0.3789063 at 80iterations 5.3026690E-03 0.1879349 at 90iterations 2.3349845E-03 7.8224182E-02 at 100iterations 1.0268638E-03 3.2272339E-02 at 110iterations 4.5314719E-04 1.4167786E-02 at 120iterations finished qdiffx linear iterations at : 08:21:31 total time elapsed so far: 8.820000 # loops : 120 mean,max change (kT/e) : 4.5314719E-04 1.4167786E-02 energy calculations done at 8.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.010000 DelPhi exited at 08:21:32 9.010u 0.210s 0:09.90 93.1% 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 08:21:32 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3105 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: 2.585122 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): -23.80900 33.77500 ymin,ymax (A): -39.12600 22.84400 zmin,zma (A): -32.36500 29.41800 x,y,z range (A): 57.58400 61.97000 61.78300 scale (grids/A): 2.585122 object centre (A): 4.983001 -8.141000 -1.473498 number of atom coordinates read : 3105 total number of charged atoms : 2952 net assigned charge : -2.999958 assigned positive charge : 457.5712 centred at (gu) : 90.59576 96.41613 100.9273 assigned negative charge : -460.5723 centred at (gu) : 90.99834 96.03643 101.4921 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 175381 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31795 grid for indexing accessible points = 1.400000 m= 80583 mr = 119503 m= 24433 mr = 62418 m= 4264 mr = 18123 m= 395 mr = 2801 m= 9 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 82026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 23600 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) : 1.723415 object centre at (A) : 4.983001 -8.141000 -1.473498 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5607336E-02 -0.4519553 midg,1,midg; midg,igrid,midg -0.4927401 -0.2213536 1,midg,midg; igrid,midg,midg 8.2825817E-02 -9.5029339E-02 gauss-seidel spectral radius is 0.9992242 estimated iterations to convergence 283 setup time was (sec) 1.660000 now iterating at: 08:21:34 rms-change max change #iterations 9.810637 318.2645 at 10iterations 5.787432 171.8114 at 20iterations 3.361088 73.37379 at 30iterations 1.946164 44.38925 at 40iterations 1.118332 23.64451 at 50iterations 0.6405895 12.72022 at 60iterations 0.3667644 7.126446 at 70iterations 0.2094488 4.076172 at 80iterations 0.1189628 2.393121 at 90iterations 6.7767151E-02 1.529010 at 100iterations 3.8535561E-02 0.7247152 at 110iterations 2.1874182E-02 0.4390612 at 120iterations 1.2443312E-02 0.2428055 at 130iterations 7.0554288E-03 0.1478271 at 140iterations 4.0058941E-03 9.5947266E-02 at 150iterations 2.2714287E-03 4.1244507E-02 at 160iterations 1.2877804E-03 2.5184631E-02 at 170iterations 7.2977017E-04 1.3244629E-02 at 180iterations finished qdiffx linear iterations at : 08:21:44 total time elapsed so far: 12.06000 # loops : 180 mean,max change (kT/e) : 7.2977017E-04 1.3244629E-02 energy calculations done at 12.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 08:21:46 12.322u 0.346s 0:13.82 91.6% 0+0k 0+0io 0pf+0w