Tue Nov 22 14:21:04 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+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 Nov 22 2011 at 14:21:08 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5769760 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): -7.189000 34.12300 ymin,ymax (A): 6.635000 51.55700 zmin,zma (A): 5.348000 67.04900 x,y,z range (A): 41.31200 44.92200 61.70100 scale (grids/A): 0.5769760 object centre (A): 13.46700 29.09600 36.19850 number of atom coordinates read : 1948 total number of charged atoms : 1816 net assigned charge : 3.000004 assigned positive charge : 290.4339 centred at (gu) : 90.05905 90.66536 90.64909 assigned negative charge : -287.4343 centred at (gu) : 90.06827 90.84889 90.65386 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4283 nv = 96 ne = 84 npr = 39884 no. pairs analyzed = 39884 no. exposed pairs = 2522 no. arc points = 17614 no. surface atoms = 852 nbur = 1096 mkacc time = 7.9999998E-02 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= 178 mr = 2232 m= 0 mr = 9 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.2100000 number of dielectric boundary points 2220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1780 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 5414 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7899879E-10 6.3607958E-10 midg,1,midg; midg,igrid,midg 2.4954985E-09 -2.1226052E-09 1,midg,midg; igrid,midg,midg 7.1869943E-10 4.9800986E-10 gauss-seidel spectral radius is 0.9844117 estimated iterations to convergence 66 setup time was (sec) 0.4300000 now iterating at: 14:21:12 rms-change max change #iterations 7.9034440E-02 17.17279 at 10iterations 5.9792446E-03 1.102516 at 20iterations 4.6430342E-04 8.6025238E-02 at 30iterations 3.5860558E-05 8.0490112E-03 at 40iterations 2.6522671E-06 4.9209595E-04 at 50iterations finished qdiffx linear iterations at : 14:21:21 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.6522671E-06 4.9209595E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 14:21:23 3.478u 0.213s 0:14.80 24.8% 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 Tue Nov 22 2011 at 14:21:24 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.730928 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): -7.189000 34.12300 ymin,ymax (A): 6.635000 51.55700 zmin,zma (A): 5.348000 67.04900 x,y,z range (A): 41.31200 44.92200 61.70100 scale (grids/A): 1.730928 object centre (A): 13.46700 29.09600 36.19850 number of atom coordinates read : 1948 total number of charged atoms : 1816 net assigned charge : 3.000004 assigned positive charge : 290.4339 centred at (gu) : 90.17729 91.99593 91.94698 assigned negative charge : -287.4343 centred at (gu) : 90.20501 92.54689 91.96197 start vw surface at 0.1100000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 46931 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17614 grid for indexing accessible points = 1.400000 m= 15181 mr = 31450 m= 1663 mr = 10972 m= 55 mr = 911 m= 0 mr = 1 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 20496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 14127 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) : 0.5769760 object centre at (A) : 13.46700 29.09600 36.19850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9862797E-02 2.2753479E-02 midg,1,midg; midg,igrid,midg 7.9976367E-03 -1.0436990E-02 1,midg,midg; igrid,midg,midg -1.9865320E-03 -3.2969010E-03 gauss-seidel spectral radius is 0.9982692 estimated iterations to convergence 191 setup time was (sec) 0.6000000 now iterating at: 14:21:25 rms-change max change #iterations 2.941401 138.3648 at 10iterations 1.251373 56.84380 at 20iterations 0.5331882 23.61282 at 30iterations 0.2262627 9.374741 at 40iterations 9.5878609E-02 3.943146 at 50iterations 4.0838093E-02 1.888906 at 60iterations 1.7376585E-02 0.6793599 at 70iterations 7.3874719E-03 0.3005655 at 80iterations 3.1281426E-03 0.1260967 at 90iterations 1.3308880E-03 5.3623408E-02 at 100iterations 5.6563062E-04 2.4274707E-02 at 110iterations 2.4100704E-04 1.0666847E-02 at 120iterations finished qdiffx linear iterations at : 14:21:42 total time elapsed so far: 6.500000 # loops : 120 mean,max change (kT/e) : 2.4100704E-04 1.0666847E-02 energy calculations done at 6.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.660000 DelPhi exited at 14:21:43 6.666u 0.153s 0:19.50 34.9% 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 Tue Nov 22 2011 at 14:21:45 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.596392 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): -7.189000 34.12300 ymin,ymax (A): 6.635000 51.55700 zmin,zma (A): 5.348000 67.04900 x,y,z range (A): 41.31200 44.92200 61.70100 scale (grids/A): 2.596392 object centre (A): 13.46700 29.09600 36.19850 number of atom coordinates read : 1948 total number of charged atoms : 1816 net assigned charge : 3.000004 assigned positive charge : 290.4339 centred at (gu) : 90.26595 92.99400 92.92043 assigned negative charge : -287.4343 centred at (gu) : 90.30751 93.82030 92.94295 start vw surface at 0.1000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 108533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17614 grid for indexing accessible points = 1.400000 m= 51093 mr = 76464 m= 16067 mr = 41261 m= 2844 mr = 12758 m= 166 mr = 1967 m= 4 mr = 61 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 0.7800000 number of dielectric boundary points 46196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 14520 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) : 1.730928 object centre at (A) : 13.46700 29.09600 36.19850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1796185 0.3445547 midg,1,midg; midg,igrid,midg 8.5135698E-02 -0.1574199 1,midg,midg; igrid,midg,midg -4.4259526E-02 -5.5949047E-02 gauss-seidel spectral radius is 0.9991329 estimated iterations to convergence 268 setup time was (sec) 1.050000 now iterating at: 14:21:51 rms-change max change #iterations 7.379729 243.9470 at 10iterations 4.088521 136.2076 at 20iterations 2.247370 58.25383 at 30iterations 1.236251 32.79839 at 40iterations 0.6795888 16.67251 at 50iterations 0.3726873 8.238340 at 60iterations 0.2038258 4.678165 at 70iterations 0.1117884 2.889118 at 80iterations 6.1116710E-02 1.368137 at 90iterations 3.3448737E-02 0.8399040 at 100iterations 1.8301098E-02 0.4596884 at 110iterations 1.0014756E-02 0.2336254 at 120iterations 5.4760394E-03 0.1266556 at 130iterations 3.0038164E-03 7.0266724E-02 at 140iterations 1.6407223E-03 4.1622162E-02 at 150iterations 8.9696661E-04 1.9873142E-02 at 160iterations 4.9113960E-04 1.2135506E-02 at 170iterations 2.6857865E-04 6.1012506E-03 at 180iterations finished qdiffx linear iterations at : 14:22:19 total time elapsed so far: 10.62000 # loops : 180 mean,max change (kT/e) : 2.6857865E-04 6.1012506E-03 energy calculations done at 10.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.80000 DelPhi exited at 14:22:21 10.798u 0.207s 0:36.20 30.3% 0+0k 0+0io 0pf+0w