Wed Dec 21 14:20:45 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 21 2011 at 14:20:45 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6062773 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): 1.924000 44.61600 ymin,ymax (A): -24.24600 24.44600 zmin,zma (A): -28.91100 29.80800 x,y,z range (A): 42.69200 48.69200 58.71900 scale (grids/A): 0.6062773 object centre (A): 23.27000 9.9999428E-02 0.4485006 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8260 centred at (gu) : 90.13872 89.94006 89.75263 assigned negative charge : -285.8263 centred at (gu) : 90.34981 89.93316 89.73864 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4892 nv = 96 ne = 84 npr = 39858 no. pairs analyzed = 39858 no. exposed pairs = 2402 no. arc points = 17202 no. surface atoms = 817 nbur = 1147 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 242 mr = 2710 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1758 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 5971 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4547773E-10 1.4440877E-09 midg,1,midg; midg,igrid,midg 8.5545648E-10 1.2777550E-09 1,midg,midg; igrid,midg,midg 7.5457880E-09 -6.1761996E-09 gauss-seidel spectral radius is 0.9858638 estimated iterations to convergence 69 setup time was (sec) 0.3400000 now iterating at: 14:20:45 rms-change max change #iterations 9.5433637E-02 17.80069 at 10iterations 8.1775459E-03 1.568672 at 20iterations 7.2152558E-04 0.1174240 at 30iterations 6.2630344E-05 1.1085033E-02 at 40iterations 5.4035004E-06 9.1797113E-04 at 50iterations finished qdiffx linear iterations at : 14:20:48 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 5.4035004E-06 9.1797113E-04 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 14:20:49 3.316u 0.177s 0:03.96 87.8% 0+0k 0+0io 6pf+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 21 2011 at 14:20:49 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.818832 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): 1.924000 44.61600 ymin,ymax (A): -24.24600 24.44600 zmin,zma (A): -28.91100 29.80800 x,y,z range (A): 42.69200 48.69200 58.71900 scale (grids/A): 1.818832 object centre (A): 23.27000 9.9999428E-02 0.4485006 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8260 centred at (gu) : 90.41612 89.82013 89.25798 assigned negative charge : -285.8263 centred at (gu) : 91.04958 89.79974 89.21589 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 53114 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17202 grid for indexing accessible points = 1.400000 m= 19150 mr = 36711 m= 2402 mr = 14528 m= 76 mr = 1395 m= 1 mr = 13 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 0.2700000 number of dielectric boundary points 22096 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 14336 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) : 0.6062773 object centre at (A) : 23.27000 9.9999428E-02 0.4485006 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0371063E-02 2.3656037E-02 midg,1,midg; midg,igrid,midg -1.7937860E-03 -1.7367752E-03 1,midg,midg; igrid,midg,midg 1.0466201E-02 -1.5941944E-02 gauss-seidel spectral radius is 0.9984295 estimated iterations to convergence 200 setup time was (sec) 0.4900000 now iterating at: 14:20:50 rms-change max change #iterations 3.229166 149.3966 at 10iterations 1.428191 54.76010 at 20iterations 0.6332172 25.06919 at 30iterations 0.2813833 11.07424 at 40iterations 0.1246080 4.359985 at 50iterations 5.5106997E-02 2.044643 at 60iterations 2.4450604E-02 0.9939098 at 70iterations 1.0796193E-02 0.4301949 at 80iterations 4.7928942E-03 0.1768317 at 90iterations 2.1328109E-03 7.6878548E-02 at 100iterations 9.4321283E-04 3.4075737E-02 at 110iterations 4.1827312E-04 1.6160965E-02 at 120iterations finished qdiffx linear iterations at : 14:20:59 total time elapsed so far: 9.810000 # loops : 120 mean,max change (kT/e) : 4.1827312E-04 1.6160965E-02 energy calculations done at 9.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.940000 DelPhi exited at 14:21:00 9.947u 0.224s 0:10.71 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 Wed Dec 21 2011 at 14:21:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.728248 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): 1.924000 44.61600 ymin,ymax (A): -24.24600 24.44600 zmin,zma (A): -28.91100 29.80800 x,y,z range (A): 42.69200 48.69200 58.71900 scale (grids/A): 2.728248 object centre (A): 23.27000 9.9999428E-02 0.4485006 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8260 centred at (gu) : 90.62422 89.73030 88.88688 assigned negative charge : -285.8263 centred at (gu) : 91.57436 89.69954 88.82391 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 123034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17202 grid for indexing accessible points = 1.400000 m= 62718 mr = 88905 m= 21750 mr = 52147 m= 4057 mr = 17815 m= 353 mr = 2936 m= 5 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 49951 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 14654 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) : 1.818832 object centre at (A) : 23.27000 9.9999428E-02 0.4485006 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1125287 0.1299416 midg,1,midg; midg,igrid,midg -5.9114374E-02 -4.8671789E-02 1,midg,midg; igrid,midg,midg 8.3592229E-02 -0.1937761 gauss-seidel spectral radius is 0.9991829 estimated iterations to convergence 276 setup time was (sec) 1.390000 now iterating at: 14:21:02 rms-change max change #iterations 7.717900 269.5623 at 10iterations 4.342134 108.2100 at 20iterations 2.434013 55.53242 at 30iterations 1.359611 29.89259 at 40iterations 0.7573898 16.86293 at 50iterations 0.4216440 8.998551 at 60iterations 0.2345328 4.999917 at 70iterations 0.1305358 2.918198 at 80iterations 7.2748490E-02 1.613777 at 90iterations 4.0472157E-02 0.8949080 at 100iterations 2.2605905E-02 0.4832382 at 110iterations 1.2566949E-02 0.2639875 at 120iterations 6.9881934E-03 0.1462097 at 130iterations 3.8941202E-03 7.7339172E-02 at 140iterations 2.1697853E-03 4.4490814E-02 at 150iterations 1.2084438E-03 2.5444031E-02 at 160iterations 6.7252899E-04 1.4469743E-02 at 170iterations 3.7558706E-04 9.1171265E-03 at 180iterations finished qdiffx linear iterations at : 14:21:18 total time elapsed so far: 17.62000 # loops : 180 mean,max change (kT/e) : 3.7558706E-04 9.1171265E-03 energy calculations done at 17.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.76000 DelPhi exited at 14:21:21 17.761u 0.601s 0:21.69 84.6% 0+0k 0+0io 0pf+0w