Wed Dec 28 11:02:51 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 Wed Dec 28 2011 at 11:02:52 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.5461211 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): -34.85200 12.02700 ymin,ymax (A): 0.1760000 42.72800 zmin,zma (A): -4.488000 60.69900 x,y,z range (A): 46.87900 42.55200 65.18700 scale (grids/A): 0.5461211 object centre (A): -11.41250 21.45200 28.10550 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 89.81198 89.41680 89.87521 assigned negative charge : -287.4003 centred at (gu) : 89.72443 89.55495 89.87117 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 3880 nv = 96 ne = 84 npr = 39669 no. pairs analyzed = 39669 no. exposed pairs = 2545 no. arc points = 17922 no. surface atoms = 859 nbur = 1111 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 = 1.568000 m= 143 mr = 1999 m= 0 mr = 10 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1814 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 5005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0849263E-10 1.3610897E-10 midg,1,midg; midg,igrid,midg 8.2117513E-10 -4.1794321E-10 1,midg,midg; igrid,midg,midg -2.7266003E-10 4.7433529E-10 gauss-seidel spectral radius is 0.9826350 estimated iterations to convergence 63 setup time was (sec) 0.7300000 now iterating at: 11:02:53 rms-change max change #iterations 5.8831282E-02 12.19369 at 10iterations 3.8189800E-03 0.7619476 at 20iterations 2.5543346E-04 5.3909034E-02 at 30iterations 1.7211294E-05 4.1337013E-03 at 40iterations 1.1522540E-06 2.5939941E-04 at 50iterations finished qdiffx linear iterations at : 11:02:59 total time elapsed so far: 7.300000 # loops : 50 mean,max change (kT/e) : 1.1522540E-06 2.5939941E-04 energy calculations done at 7.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 11:03:01 7.476u 0.672s 0:09.58 84.9% 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 Wed Dec 28 2011 at 11:03:01 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.638363 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): -34.85200 12.02700 ymin,ymax (A): 0.1760000 42.72800 zmin,zma (A): -4.488000 60.69900 x,y,z range (A): 46.87900 42.55200 65.18700 scale (grids/A): 1.638363 object centre (A): -11.41250 21.45200 28.10550 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 89.43606 88.25036 89.62557 assigned negative charge : -287.4003 centred at (gu) : 89.17371 88.66505 89.61343 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 42498 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17922 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 13190 mr = 28251 m= 1333 mr = 9450 m= 39 mr = 702 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 952 time to turn everything in is 0.4600000 number of dielectric boundary points 18655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 250 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 14151 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) : 0.5461211 object centre at (A) : -11.41250 21.45200 28.10550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7082538E-02 1.6757399E-02 midg,1,midg; midg,igrid,midg 2.0871740E-03 -4.9996274E-03 1,midg,midg; igrid,midg,midg -2.8146412E-03 -9.8229747E-04 gauss-seidel spectral radius is 0.9980758 estimated iterations to convergence 181 setup time was (sec) 0.9700000 now iterating at: 11:03:03 rms-change max change #iterations 2.622871 136.8391 at 10iterations 1.066404 47.53626 at 20iterations 0.4335912 21.99352 at 30iterations 0.1757578 8.857433 at 40iterations 7.1206450E-02 3.017639 at 50iterations 2.8867701E-02 1.275053 at 60iterations 1.1703853E-02 0.5084629 at 70iterations 4.7619999E-03 0.2170043 at 80iterations 1.9300026E-03 8.1663609E-02 at 90iterations 7.8353635E-04 3.4682751E-02 at 100iterations 3.1959385E-04 1.4265060E-02 at 110iterations 1.2965979E-04 5.4113865E-03 at 120iterations finished qdiffx linear iterations at : 11:03:21 total time elapsed so far: 18.92000 # loops : 120 mean,max change (kT/e) : 1.2965979E-04 5.4113865E-03 energy calculations done at 18.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.09000 DelPhi exited at 11:03:21 19.090u 0.859s 0:20.31 98.1% 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 Wed Dec 28 2011 at 11:03:22 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.457545 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): -34.85200 12.02700 ymin,ymax (A): 0.1760000 42.72800 zmin,zma (A): -4.488000 60.69900 x,y,z range (A): 46.87900 42.55200 65.18700 scale (grids/A): 2.457545 object centre (A): -11.41250 21.45200 28.10550 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 289.4000 centred at (gu) : 89.15406 87.37553 89.43839 assigned negative charge : -287.4003 centred at (gu) : 88.76057 87.99756 89.42030 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 98396 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17922 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 45494 mr = 68727 m= 13063 mr = 36633 m= 2197 mr = 10243 m= 165 mr = 1514 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 3167 time to turn everything in is 1.050000 number of dielectric boundary points 42128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 14685 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) : 1.638363 object centre at (A) : -11.41250 21.45200 28.10550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2253530 0.1989468 midg,1,midg; midg,igrid,midg 7.5199045E-03 -7.8162722E-02 1,midg,midg; igrid,midg,midg -5.3568441E-02 -2.5148900E-02 gauss-seidel spectral radius is 0.9990659 estimated iterations to convergence 259 setup time was (sec) 1.680000 now iterating at: 11:03:24 rms-change max change #iterations 6.715740 325.2792 at 10iterations 3.628709 166.2306 at 20iterations 1.960606 53.62936 at 30iterations 1.052327 30.85226 at 40iterations 0.5649967 15.52904 at 50iterations 0.3028409 7.874399 at 60iterations 0.1621844 3.790546 at 70iterations 8.6701229E-02 2.192923 at 80iterations 4.6372414E-02 1.309139 at 90iterations 2.4847511E-02 0.6082153 at 100iterations 1.3298344E-02 0.3788948 at 110iterations 7.0986650E-03 0.1884969 at 120iterations 3.7937684E-03 9.6418381E-02 at 130iterations 2.0356472E-03 5.3002298E-02 at 140iterations 1.0834220E-03 2.6358604E-02 at 150iterations 5.8079872E-04 1.4411926E-02 at 160iterations 3.1028211E-04 8.4836483E-03 at 170iterations 1.6623388E-04 4.1260719E-03 at 180iterations finished qdiffx linear iterations at : 11:03:51 total time elapsed so far: 28.78000 # loops : 180 mean,max change (kT/e) : 1.6623388E-04 4.1260719E-03 energy calculations done at 28.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 28.96000 DelPhi exited at 11:03:52 28.966u 0.895s 0:30.25 98.6% 0+0k 0+0io 0pf+0w