Tue Oct 11 03:48:30 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 Tue Oct 11 2011 at 03:48:30 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 = 2701 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6607766 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): -9.479000 36.59500 ymin,ymax (A): -26.88700 21.78100 zmin,zma (A): -8.257000 45.61900 x,y,z range (A): 46.07400 48.66800 53.87600 scale (grids/A): 0.6607766 object centre (A): 13.55800 -2.552999 18.68100 number of atom coordinates read : 2701 total number of charged atoms : 2626 net assigned charge : 2.500019 assigned positive charge : 421.6366 centred at (gu) : 89.40670 90.54874 91.36439 assigned negative charge : -419.1372 centred at (gu) : 89.10213 90.44090 91.36754 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8179 nv = 96 ne = 84 npr = 51561 no. pairs analyzed = 51561 no. exposed pairs = 3504 no. arc points = 24360 no. surface atoms = 1163 nbur = 1538 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 4557 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3500000 number of dielectric boundary points 4022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2306 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9557 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7760241E-09 8.1921492E-09 midg,1,midg; midg,igrid,midg -1.4924032E-08 3.3763989E-08 1,midg,midg; igrid,midg,midg -6.9838741E-08 6.2703663E-08 gauss-seidel spectral radius is 0.9881427 estimated iterations to convergence 75 setup time was (sec) 0.6200000 now iterating at: 03:48:31 rms-change max change #iterations 0.1733969 27.12571 at 10iterations 1.8888922E-02 2.682660 at 20iterations 2.0350053E-03 0.2460346 at 30iterations 2.3352442E-04 2.9764175E-02 at 40iterations 3.1346044E-05 4.3296814E-03 at 50iterations finished qdiffx linear iterations at : 03:48:34 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 3.1346044E-05 4.3296814E-03 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 03:48:35 4.134u 0.270s 0:04.93 89.2% 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 Oct 11 2011 at 03:48:35 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 = 2701 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.982330 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): -9.479000 36.59500 ymin,ymax (A): -26.88700 21.78100 zmin,zma (A): -8.257000 45.61900 x,y,z range (A): 46.07400 48.66800 53.87600 scale (grids/A): 1.982330 object centre (A): 13.55800 -2.552999 18.68100 number of atom coordinates read : 2701 total number of charged atoms : 2626 net assigned charge : 2.500019 assigned positive charge : 421.6366 centred at (gu) : 88.21928 91.64556 94.09286 assigned negative charge : -419.1372 centred at (gu) : 87.30628 91.32245 94.10213 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 87625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24360 grid for indexing accessible points = 1.400000 m= 34153 mr = 61316 m= 6031 mr = 25593 m= 418 mr = 3947 m= 3 mr = 179 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 414 time to turn everything in is 0.7700000 number of dielectric boundary points 37195 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 20703 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) : 0.6607766 object centre at (A) : 13.55800 -2.552999 18.68100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6734557E-03 6.4852699E-03 midg,1,midg; midg,igrid,midg -1.8446138E-02 4.9502468E-03 1,midg,midg; igrid,midg,midg -3.7290975E-02 6.5140538E-02 gauss-seidel spectral radius is 0.9987552 estimated iterations to convergence 224 setup time was (sec) 1.100000 now iterating at: 03:48:36 rms-change max change #iterations 4.815373 231.0008 at 10iterations 2.344566 74.08714 at 20iterations 1.136489 32.15205 at 30iterations 0.5507780 18.16990 at 40iterations 0.2682525 7.519928 at 50iterations 0.1299376 4.085193 at 60iterations 6.3266531E-02 1.966406 at 70iterations 3.0609204E-02 0.9329014 at 80iterations 1.4843517E-02 0.4816475 at 90iterations 7.2288830E-03 0.2018585 at 100iterations 3.5041028E-03 9.7397089E-02 at 110iterations 1.7059199E-03 4.9529076E-02 at 120iterations finished qdiffx linear iterations at : 03:48:45 total time elapsed so far: 9.710000 # loops : 120 mean,max change (kT/e) : 1.7059199E-03 4.9529076E-02 energy calculations done at 9.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.890000 DelPhi exited at 03:48:46 9.889u 0.301s 0:10.64 95.6% 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 Oct 11 2011 at 03:48:47 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 = 2701 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.973495 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): -9.479000 36.59500 ymin,ymax (A): -26.88700 21.78100 zmin,zma (A): -8.257000 45.61900 x,y,z range (A): 46.07400 48.66800 53.87600 scale (grids/A): 2.973495 object centre (A): 13.55800 -2.552999 18.68100 number of atom coordinates read : 2701 total number of charged atoms : 2626 net assigned charge : 2.500019 assigned positive charge : 421.6366 centred at (gu) : 87.32873 92.46825 96.13920 assigned negative charge : -419.1372 centred at (gu) : 85.95939 91.98357 96.15319 start vw surface at 0.1600000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 201906 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24360 grid for indexing accessible points = 1.400000 m= 107822 mr = 147768 m= 42214 mr = 89195 m= 11245 mr = 34324 m= 1860 mr = 8634 m= 139 mr = 1314 m= 6 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 1340 time to turn everything in is 2.050000 number of dielectric boundary points 83895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 21008 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) : 1.982330 object centre at (A) : 13.55800 -2.552999 18.68100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0707593E-03 0.2719103 midg,1,midg; midg,igrid,midg -0.2339482 5.8393847E-02 1,midg,midg; igrid,midg,midg -0.3093799 0.5523644 gauss-seidel spectral radius is 0.9992973 estimated iterations to convergence 298 setup time was (sec) 2.380000 now iterating at: 03:48:49 rms-change max change #iterations 11.12878 355.4765 at 10iterations 6.611444 139.6434 at 20iterations 3.913954 87.57178 at 30iterations 2.314489 45.99256 at 40iterations 1.362523 24.53976 at 50iterations 0.8031231 14.88019 at 60iterations 0.4719661 9.035217 at 70iterations 0.2767927 5.359997 at 80iterations 0.1621236 2.618958 at 90iterations 9.4915561E-02 1.621552 at 100iterations 5.5630114E-02 1.034817 at 110iterations 3.2501992E-02 0.5486526 at 120iterations 1.9018099E-02 0.3354645 at 130iterations 1.1104567E-02 0.2115402 at 140iterations 6.4854864E-03 0.1072595 at 150iterations 3.7922654E-03 6.2179565E-02 at 160iterations 2.2254686E-03 3.7630200E-02 at 170iterations 1.3018614E-03 2.3864269E-02 at 180iterations finished qdiffx linear iterations at : 03:49:04 total time elapsed so far: 16.72000 # loops : 180 mean,max change (kT/e) : 1.3018614E-03 2.3864269E-02 energy calculations done at 16.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.90000 DelPhi exited at 03:49:04 16.903u 0.320s 0:17.75 97.0% 0+0k 0+0io 0pf+0w