Tue Oct 11 06:57:43 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+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 Oct 11 2011 at 06:57:43 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3144 !!! WARNING: UMP 317 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5479031 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): -19.78100 45.19400 ymin,ymax (A): 19.67100 77.73200 zmin,zma (A): -70.23000 -20.87600 x,y,z range (A): 64.97500 58.06100 49.35400 scale (grids/A): 0.5479031 object centre (A): 12.70650 48.70150 -45.55300 number of atom coordinates read : 3144 total number of charged atoms : 2999 net assigned charge : -3.599989 assigned positive charge : 463.6274 centred at (gu) : 89.49868 89.68432 90.09620 assigned negative charge : -467.2279 centred at (gu) : 89.55959 89.91021 90.07478 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6034 nv = 96 ne = 84 npr = 64976 no. pairs analyzed = 64976 no. exposed pairs = 3947 no. arc points = 27893 no. surface atoms = 1334 nbur = 1810 mkacc time = 0.2200000 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= 255 mr = 3106 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 3169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2798 ## 348 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 7940 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9999287E-10 -8.9609702E-11 midg,1,midg; midg,igrid,midg 1.5174680E-09 -1.8425020E-09 1,midg,midg; igrid,midg,midg 2.3503238E-10 -6.2670019E-10 gauss-seidel spectral radius is 0.9828386 estimated iterations to convergence 63 setup time was (sec) 0.8100000 now iterating at: 06:57:45 rms-change max change #iterations 7.9195127E-02 14.27617 at 10iterations 5.2336529E-03 1.012329 at 20iterations 3.5333424E-04 6.0180664E-02 at 30iterations 2.3836332E-05 3.7155151E-03 at 40iterations 1.6739705E-06 2.5177002E-04 at 50iterations finished qdiffx linear iterations at : 06:57:48 total time elapsed so far: 4.350000 # loops : 50 mean,max change (kT/e) : 1.6739705E-06 2.5177002E-04 energy calculations done at 4.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.570000 DelPhi exited at 06:57:49 4.573u 0.398s 0:05.61 88.4% 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 06:57:49 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3144 !!! WARNING: UMP 317 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.643709 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): -19.78100 45.19400 ymin,ymax (A): 19.67100 77.73200 zmin,zma (A): -70.23000 -20.87600 x,y,z range (A): 64.97500 58.06100 49.35400 scale (grids/A): 1.643709 object centre (A): 12.70650 48.70150 -45.55300 number of atom coordinates read : 3144 total number of charged atoms : 2999 net assigned charge : -3.599989 assigned positive charge : 463.6274 centred at (gu) : 88.49568 89.05231 90.28788 assigned negative charge : -467.2279 centred at (gu) : 88.67815 89.73000 90.22409 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 66715 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27893 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21297 mr = 44912 m= 2402 mr = 14931 m= 61 mr = 1270 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.7100000 number of dielectric boundary points 29362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 280 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 23017 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) : 0.5479031 object centre at (A) : 12.70650 48.70150 -45.55300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8981704E-03 1.2768062E-02 midg,1,midg; midg,igrid,midg 6.9984334E-04 -1.3901153E-02 1,midg,midg; igrid,midg,midg 4.4478206E-03 -3.4232199E-02 gauss-seidel spectral radius is 0.9982305 estimated iterations to convergence 189 setup time was (sec) 1.030000 now iterating at: 06:57:51 rms-change max change #iterations 3.486988 152.7294 at 10iterations 1.461952 58.31660 at 20iterations 0.6165251 22.48922 at 30iterations 0.2602822 8.726901 at 40iterations 0.1096978 3.787424 at 50iterations 4.6308242E-02 1.548580 at 60iterations 1.9573959E-02 0.6720829 at 70iterations 8.2343668E-03 0.2578201 at 80iterations 3.4717948E-03 0.1497307 at 90iterations 1.4624402E-03 4.7355652E-02 at 100iterations 6.1876408E-04 2.0713806E-02 at 110iterations 2.6137961E-04 8.6936951E-03 at 120iterations finished qdiffx linear iterations at : 06:58:00 total time elapsed so far: 9.970000 # loops : 120 mean,max change (kT/e) : 2.6137961E-04 8.6936951E-03 energy calculations done at 9.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.18000 DelPhi exited at 06:58:00 10.182u 0.471s 0:11.12 95.7% 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 06:58:00 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3144 !!! WARNING: UMP 317 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.465564 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): -19.78100 45.19400 ymin,ymax (A): 19.67100 77.73200 zmin,zma (A): -70.23000 -20.87600 x,y,z range (A): 64.97500 58.06100 49.35400 scale (grids/A): 2.465564 object centre (A): 12.70650 48.70150 -45.55300 number of atom coordinates read : 3144 total number of charged atoms : 2999 net assigned charge : -3.599989 assigned positive charge : 463.6274 centred at (gu) : 87.74339 88.57841 90.43176 assigned negative charge : -467.2279 centred at (gu) : 88.01714 89.59494 90.33600 start vw surface at 0.1800000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 154864 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27893 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 72010 mr = 110155 m= 22141 mr = 56922 m= 3849 mr = 17218 m= 254 mr = 2564 m= 2 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 140 time to turn everything in is 1.730000 number of dielectric boundary points 66152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 23967 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) : 1.643709 object centre at (A) : 12.70650 48.70150 -45.55300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9634097E-02 0.2399452 midg,1,midg; midg,igrid,midg -8.8735186E-03 -0.1320267 1,midg,midg; igrid,midg,midg 1.3784124E-02 -0.6869859 gauss-seidel spectral radius is 0.9991561 estimated iterations to convergence 272 setup time was (sec) 2.090000 now iterating at: 06:58:03 rms-change max change #iterations 8.932856 283.0112 at 10iterations 5.037744 119.7459 at 20iterations 2.827547 71.49361 at 30iterations 1.582628 35.57838 at 40iterations 0.8802484 21.57355 at 50iterations 0.4892260 10.73579 at 60iterations 0.2722054 5.151193 at 70iterations 0.1507616 3.378620 at 80iterations 8.3574794E-02 1.769842 at 90iterations 4.6271037E-02 0.9312592 at 100iterations 2.5569666E-02 0.5039992 at 110iterations 1.4123480E-02 0.2772121 at 120iterations 7.8308368E-03 0.1824894 at 130iterations 4.3176510E-03 8.5201979E-02 at 140iterations 2.3843513E-03 5.1662445E-02 at 150iterations 1.3181111E-03 2.6670456E-02 at 160iterations 7.2880986E-04 1.5385628E-02 at 170iterations 4.0229992E-04 8.3236694E-03 at 180iterations finished qdiffx linear iterations at : 06:58:18 total time elapsed so far: 16.90000 # loops : 180 mean,max change (kT/e) : 4.0229992E-04 8.3236694E-03 energy calculations done at 16.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.11000 DelPhi exited at 06:58:19 17.110u 0.479s 0:19.08 92.1% 0+0k 0+0io 0pf+0w