Mon Oct 10 17:02:30 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 17:02:30 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 = 3269 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: 0.5775658 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): -50.84300 7.059000 ymin,ymax (A): 37.69900 93.51400 zmin,zma (A): -4.582000 57.05600 x,y,z range (A): 57.90200 55.81500 61.63800 scale (grids/A): 0.5775658 object centre (A): -21.89200 65.60650 26.23700 number of atom coordinates read : 3269 total number of charged atoms : 3130 net assigned charge : 7.500017 assigned positive charge : 497.8887 centred at (gu) : 89.89756 90.86917 87.87100 assigned negative charge : -490.3897 centred at (gu) : 89.90438 90.94157 87.87222 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7149 nv = 96 ne = 84 npr = 66115 no. pairs analyzed = 66115 no. exposed pairs = 4026 no. arc points = 28667 no. surface atoms = 1355 nbur = 1914 mkacc time = 0.1100000 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 = 1.512000 m= 312 mr = 3823 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.2300000 number of dielectric boundary points 3612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2968 ## 381 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9134 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5152391E-09 9.2008456E-10 midg,1,midg; midg,igrid,midg 2.5404054E-09 -1.5929813E-10 1,midg,midg; igrid,midg,midg 1.7026763E-09 1.3285177E-09 gauss-seidel spectral radius is 0.9845514 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 17:02:31 rms-change max change #iterations 0.1015356 14.83636 at 10iterations 7.9605347E-03 1.386082 at 20iterations 6.0897943E-04 8.5051537E-02 at 30iterations 4.7275633E-05 7.0343018E-03 at 40iterations 3.6965948E-06 5.3596497E-04 at 50iterations finished qdiffx linear iterations at : 17:02:33 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 3.6965948E-06 5.3596497E-04 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 17:02:35 3.370u 0.170s 0:04.53 78.1% 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 Mon Oct 10 2011 at 17:02:35 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 = 3269 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: 1.732697 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): -50.84300 7.059000 ymin,ymax (A): 37.69900 93.51400 zmin,zma (A): -4.582000 57.05600 x,y,z range (A): 57.90200 55.81500 61.63800 scale (grids/A): 1.732697 object centre (A): -21.89200 65.60650 26.23700 number of atom coordinates read : 3269 total number of charged atoms : 3130 net assigned charge : 7.500017 assigned positive charge : 497.8887 centred at (gu) : 89.69193 92.60644 83.61182 assigned negative charge : -490.3897 centred at (gu) : 89.71287 92.82432 83.61597 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 77797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28667 grid for indexing accessible points = 1.400000 m= 25896 mr = 52948 m= 3043 mr = 18498 m= 97 mr = 1672 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1596 time to turn everything in is 0.3900000 number of dielectric boundary points 33692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 296 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 24283 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) : 0.5775658 object centre at (A) : -21.89200 65.60650 26.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9227487E-04 1.7367758E-02 midg,1,midg; midg,igrid,midg 2.3750760E-02 7.8037162E-03 1,midg,midg; igrid,midg,midg 1.8392593E-03 3.3165097E-02 gauss-seidel spectral radius is 0.9984174 estimated iterations to convergence 199 setup time was (sec) 0.6100000 now iterating at: 17:02:35 rms-change max change #iterations 3.970646 160.0708 at 10iterations 1.743992 60.96017 at 20iterations 0.7654958 25.86236 at 30iterations 0.3387221 10.95421 at 40iterations 0.1497653 4.913374 at 50iterations 6.6141374E-02 2.112942 at 60iterations 2.9171174E-02 0.9329357 at 70iterations 1.2889690E-02 0.4134598 at 80iterations 5.6757848E-03 0.1785916 at 90iterations 2.5134624E-03 8.2676411E-02 at 100iterations 1.1105035E-03 3.5499573E-02 at 110iterations 4.9036642E-04 1.7199516E-02 at 120iterations finished qdiffx linear iterations at : 17:02:42 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 4.9036642E-04 1.7199516E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 17:02:43 7.704u 0.189s 0:08.78 89.7% 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 17:02:43 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 = 3269 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: 2.599046 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): -50.84300 7.059000 ymin,ymax (A): 37.69900 93.51400 zmin,zma (A): -4.582000 57.05600 x,y,z range (A): 57.90200 55.81500 61.63800 scale (grids/A): 2.599046 object centre (A): -21.89200 65.60650 26.23700 number of atom coordinates read : 3269 total number of charged atoms : 3130 net assigned charge : 7.500017 assigned positive charge : 497.8887 centred at (gu) : 89.53744 93.90955 80.41759 assigned negative charge : -490.3897 centred at (gu) : 89.56915 94.23634 80.42383 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 180169 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28667 grid for indexing accessible points = 1.400000 m= 87015 mr = 128987 m= 26937 mr = 70040 m= 5038 mr = 20828 m= 493 mr = 3568 m= 17 mr = 282 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 5534 time to turn everything in is 0.9500000 number of dielectric boundary points 75964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 25034 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) : 1.732697 object centre at (A) : -21.89200 65.60650 26.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9604501E-02 0.1743470 midg,1,midg; midg,igrid,midg 0.3188230 6.4845271E-02 1,midg,midg; igrid,midg,midg -3.0763881E-02 0.5125018 gauss-seidel spectral radius is 0.9992144 estimated iterations to convergence 282 setup time was (sec) 1.180000 now iterating at: 17:02:45 rms-change max change #iterations 9.891632 282.5269 at 10iterations 5.653840 152.8373 at 20iterations 3.220090 61.51710 at 30iterations 1.832342 41.02095 at 40iterations 1.037327 19.42987 at 50iterations 0.5866591 10.89474 at 60iterations 0.3311611 6.644883 at 70iterations 0.1874596 3.394976 at 80iterations 0.1058792 1.838317 at 90iterations 5.9636045E-02 1.092016 at 100iterations 3.3700962E-02 0.6132269 at 110iterations 1.9006163E-02 0.3373718 at 120iterations 1.0717659E-02 0.1869287 at 130iterations 6.0489275E-03 0.1082256 at 140iterations 3.4109566E-03 6.0615540E-02 at 150iterations 1.9226557E-03 4.0122986E-02 at 160iterations 1.0868774E-03 2.0064354E-02 at 170iterations 6.1319181E-04 1.0663986E-02 at 180iterations finished qdiffx linear iterations at : 17:02:57 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 6.1319181E-04 1.0663986E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 17:02:57 12.474u 0.202s 0:13.69 92.5% 0+0k 0+0io 0pf+0w