Mon Oct 10 14:40:52 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 14:40:52 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2462 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5911952 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): -2.936000 44.05400 ymin,ymax (A): 12.62700 72.84400 zmin,zma (A): 54.70000 106.8060 x,y,z range (A): 46.99000 60.21700 52.10600 scale (grids/A): 0.5911952 object centre (A): 20.55900 42.73550 80.75300 number of atom coordinates read : 2462 total number of charged atoms : 2305 net assigned charge : 1.000006 assigned positive charge : 360.7971 centred at (gu) : 88.88692 90.37969 89.93687 assigned negative charge : -359.7976 centred at (gu) : 88.78025 90.25307 89.93771 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5745 nv = 96 ne = 84 npr = 48792 no. pairs analyzed = 48792 no. exposed pairs = 3348 no. arc points = 23633 no. surface atoms = 1120 nbur = 1342 mkacc time = 0.1200000 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 = 1.456000 m= 263 mr = 2857 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2217 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7026 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7058306E-10 3.1828448E-10 midg,1,midg; midg,igrid,midg -2.6965261E-09 3.8688972E-09 1,midg,midg; igrid,midg,midg -3.1574117E-09 2.3519431E-09 gauss-seidel spectral radius is 0.9851913 estimated iterations to convergence 67 setup time was (sec) 0.5300000 now iterating at: 14:40:53 rms-change max change #iterations 9.6834660E-02 19.62634 at 10iterations 7.7686082E-03 1.272255 at 20iterations 6.3504407E-04 0.1052246 at 30iterations 5.2207874E-05 9.0470314E-03 at 40iterations 4.2657480E-06 6.8664551E-04 at 50iterations finished qdiffx linear iterations at : 14:40:57 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 4.2657480E-06 6.8664551E-04 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 14:40:57 4.426u 0.427s 0:05.15 93.9% 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 Mon Oct 10 2011 at 14:40:57 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2462 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: 1.773585 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): -2.936000 44.05400 ymin,ymax (A): 12.62700 72.84400 zmin,zma (A): 54.70000 106.8060 x,y,z range (A): 46.99000 60.21700 52.10600 scale (grids/A): 1.773585 object centre (A): 20.55900 42.73550 80.75300 number of atom coordinates read : 2462 total number of charged atoms : 2305 net assigned charge : 1.000006 assigned positive charge : 360.7971 centred at (gu) : 86.66044 91.13872 89.81052 assigned negative charge : -359.7976 centred at (gu) : 86.34032 90.75901 89.81286 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63293 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23633 grid for indexing accessible points = 1.400000 m= 20030 mr = 42209 m= 2269 mr = 13399 m= 117 mr = 1034 m= 0 mr = 20 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 29047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17926 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) : 0.5911952 object centre at (A) : 20.55900 42.73550 80.75300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1842368E-03 4.0852637E-03 midg,1,midg; midg,igrid,midg 2.9291892E-03 -2.0787956E-03 1,midg,midg; igrid,midg,midg -2.1477160E-03 4.7374940E-03 gauss-seidel spectral radius is 0.9984212 estimated iterations to convergence 200 setup time was (sec) 0.8400000 now iterating at: 14:40:59 rms-change max change #iterations 3.552327 171.1499 at 10iterations 1.554428 61.40946 at 20iterations 0.6872619 24.08587 at 30iterations 0.3031006 10.18597 at 40iterations 0.1336644 4.838591 at 50iterations 5.8979645E-02 2.226226 at 60iterations 2.6130291E-02 0.9238068 at 70iterations 1.1541843E-02 0.3863373 at 80iterations 5.1144296E-03 0.1897058 at 90iterations 2.2641758E-03 7.7884674E-02 at 100iterations 9.9711609E-04 3.5788536E-02 at 110iterations 4.4257022E-04 1.5295982E-02 at 120iterations finished qdiffx linear iterations at : 14:41:08 total time elapsed so far: 10.27000 # loops : 120 mean,max change (kT/e) : 4.4257022E-04 1.5295982E-02 energy calculations done at 10.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.43000 DelPhi exited at 14:41:09 10.436u 0.447s 0:11.19 97.1% 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 14:41:09 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2462 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.660378 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): -2.936000 44.05400 ymin,ymax (A): 12.62700 72.84400 zmin,zma (A): 54.70000 106.8060 x,y,z range (A): 46.99000 60.21700 52.10600 scale (grids/A): 2.660378 object centre (A): 20.55900 42.73550 80.75300 number of atom coordinates read : 2462 total number of charged atoms : 2305 net assigned charge : 1.000006 assigned positive charge : 360.7971 centred at (gu) : 84.99049 91.70788 89.71565 assigned negative charge : -359.7976 centred at (gu) : 84.51047 91.13837 89.71916 start vw surface at 0.1200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 146601 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23633 grid for indexing accessible points = 1.400000 m= 68040 mr = 103178 m= 20214 mr = 53294 m= 3568 mr = 14538 m= 396 mr = 2142 m= 17 mr = 227 m= 0 mr = 4 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 65453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 18435 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) : 1.773585 object centre at (A) : 20.55900 42.73550 80.75300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1562444 8.7902755E-02 midg,1,midg; midg,igrid,midg 0.1521844 -0.1981431 1,midg,midg; igrid,midg,midg 9.8208627E-03 3.8167860E-02 gauss-seidel spectral radius is 0.9992025 estimated iterations to convergence 280 setup time was (sec) 1.650000 now iterating at: 14:41:11 rms-change max change #iterations 8.805509 295.5491 at 10iterations 5.107982 150.2999 at 20iterations 2.930165 92.72174 at 30iterations 1.677000 48.72907 at 40iterations 0.9556340 22.10605 at 50iterations 0.5418464 12.02282 at 60iterations 0.3074547 7.120494 at 70iterations 0.1736858 3.613447 at 80iterations 9.8523438E-02 2.267239 at 90iterations 5.5389944E-02 1.337809 at 100iterations 3.1273648E-02 0.6186905 at 110iterations 1.7639240E-02 0.3724728 at 120iterations 9.9326614E-03 0.2012682 at 130iterations 5.5868388E-03 0.1144743 at 140iterations 3.1464007E-03 6.8367004E-02 at 150iterations 1.7724364E-03 3.4927368E-02 at 160iterations 9.9507184E-04 2.0601273E-02 at 170iterations 5.6088949E-04 1.2289047E-02 at 180iterations finished qdiffx linear iterations at : 14:41:26 total time elapsed so far: 17.23000 # loops : 180 mean,max change (kT/e) : 5.6088949E-04 1.2289047E-02 energy calculations done at 17.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.39000 DelPhi exited at 14:41:27 17.399u 0.462s 0:18.23 97.9% 0+0k 0+0io 0pf+0w