Sun Oct 9 15:36:07 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 Sun Oct 9 2011 at 15:36:07 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 = 5852 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5101456 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): 154.0140 222.8590 ymin,ymax (A): 90.86000 158.5390 zmin,zma (A): -2.145000 67.63900 x,y,z range (A): 68.84499 67.67900 69.78400 scale (grids/A): 0.5101456 object centre (A): 188.4365 124.6995 32.74700 number of atom coordinates read : 5852 total number of charged atoms : 5676 net assigned charge : -2.499967 assigned positive charge : 897.7195 centred at (gu) : 89.18532 89.33882 89.35505 assigned negative charge : -900.2278 centred at (gu) : 89.20518 89.40464 89.32548 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 9309 nv = 96 ne = 84 npr = 120843 no. pairs analyzed = 120843 no. exposed pairs = 6784 no. arc points = 46192 no. surface atoms = 2264 nbur = 3588 mkacc time = 0.2100000 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 = 1.652000 m= 285 mr = 5063 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3600000 number of dielectric boundary points 4524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4507 ## 678 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 12596 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5588461E-10 4.8749893E-11 midg,1,midg; midg,igrid,midg 2.0676477E-10 -2.0889321E-10 1,midg,midg; igrid,midg,midg 3.4385390E-11 -8.0761765E-11 gauss-seidel spectral radius is 0.9804091 estimated iterations to convergence 59 setup time was (sec) 0.5500000 now iterating at: 15:36:08 rms-change max change #iterations 7.4982189E-02 11.01671 at 10iterations 4.9105943E-03 0.6435165 at 20iterations 6.0549186E-04 8.4472656E-02 at 30iterations 1.2597691E-04 1.7135620E-02 at 40iterations 2.9383415E-05 3.8146973E-03 at 50iterations finished qdiffx linear iterations at : 15:36:10 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 2.9383415E-05 3.8146973E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 15:36:11 3.613u 0.215s 0:04.21 90.7% 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 Sun Oct 9 2011 at 15:36:11 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 = 5852 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: 1.530437 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): 154.0140 222.8590 ymin,ymax (A): 90.86000 158.5390 zmin,zma (A): -2.145000 67.63900 x,y,z range (A): 68.84499 67.67900 69.78400 scale (grids/A): 1.530437 object centre (A): 188.4365 124.6995 32.74700 number of atom coordinates read : 5852 total number of charged atoms : 5676 net assigned charge : -2.499967 assigned positive charge : 897.7195 centred at (gu) : 87.55411 88.01479 88.06297 assigned negative charge : -900.2278 centred at (gu) : 87.61546 88.21382 87.97632 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 106446 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46192 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 29948 mr = 75531 m= 2443 mr = 20364 m= 51 mr = 1059 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1797 time to turn everything in is 0.5100000 number of dielectric boundary points 41934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 642 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 42500 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) : 0.5101456 object centre at (A) : 188.4365 124.6995 32.74700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8755468E-03 -1.2136630E-02 midg,1,midg; midg,igrid,midg 1.1098281E-02 -8.9701554E-03 1,midg,midg; igrid,midg,midg -2.2136303E-02 2.0620211E-03 gauss-seidel spectral radius is 0.9981804 estimated iterations to convergence 186 setup time was (sec) 0.7300000 now iterating at: 15:36:12 rms-change max change #iterations 4.301446 159.7357 at 10iterations 1.792596 52.54812 at 20iterations 0.7459805 24.33614 at 30iterations 0.3122080 10.98929 at 40iterations 0.1306157 3.829685 at 50iterations 5.4574627E-02 1.550980 at 60iterations 2.2869810E-02 0.7843895 at 70iterations 9.6251043E-03 0.3009338 at 80iterations 4.0658205E-03 0.1240234 at 90iterations 1.7316700E-03 5.2799225E-02 at 100iterations 7.4460334E-04 2.2415161E-02 at 110iterations 3.2966238E-04 1.0276794E-02 at 120iterations finished qdiffx linear iterations at : 15:36:19 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 3.2966238E-04 1.0276794E-02 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 15:36:20 8.178u 0.218s 0:08.69 96.4% 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 Sun Oct 9 2011 at 15:36:20 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 = 5852 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: 2.295655 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): 154.0140 222.8590 ymin,ymax (A): 90.86000 158.5390 zmin,zma (A): -2.145000 67.63900 x,y,z range (A): 68.84499 67.67900 69.78400 scale (grids/A): 2.295655 object centre (A): 188.4365 124.6995 32.74700 number of atom coordinates read : 5852 total number of charged atoms : 5676 net assigned charge : -2.499967 assigned positive charge : 897.7195 centred at (gu) : 86.33089 87.02196 87.09388 assigned negative charge : -900.2278 centred at (gu) : 86.42295 87.32057 86.96429 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 248852 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46192 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 109399 mr = 185565 m= 26810 mr = 86750 m= 3485 mr = 19528 m= 147 mr = 2160 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 5852 time to turn everything in is 1.230000 number of dielectric boundary points 94662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 45294 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) : 1.530437 object centre at (A) : 188.4365 124.6995 32.74700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4863103 -0.2415658 midg,1,midg; midg,igrid,midg 0.2359406 -0.1471848 1,midg,midg; igrid,midg,midg -0.5703542 -5.4437225E-03 gauss-seidel spectral radius is 0.9991947 estimated iterations to convergence 278 setup time was (sec) 1.490000 now iterating at: 15:36:21 rms-change max change #iterations 11.49352 251.5608 at 10iterations 6.611424 142.4552 at 20iterations 3.784611 83.05493 at 30iterations 2.151089 44.56114 at 40iterations 1.220385 28.35986 at 50iterations 0.6897832 13.15612 at 60iterations 0.3891723 6.926891 at 70iterations 0.2196585 3.688692 at 80iterations 0.1239408 2.059656 at 90iterations 6.9550693E-02 1.199773 at 100iterations 3.9181232E-02 0.6673412 at 110iterations 2.2007843E-02 0.3822904 at 120iterations 1.2389624E-02 0.2171974 at 130iterations 6.9538853E-03 0.1207223 at 140iterations 3.9088619E-03 6.4224243E-02 at 150iterations 2.1996512E-03 4.0365219E-02 at 160iterations 1.2376923E-03 2.0309448E-02 at 170iterations 6.9671770E-04 1.1381149E-02 at 180iterations finished qdiffx linear iterations at : 15:36:33 total time elapsed so far: 13.43000 # loops : 180 mean,max change (kT/e) : 6.9671770E-04 1.1381149E-02 energy calculations done at 13.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.56000 DelPhi exited at 15:36:34 13.566u 0.208s 0:14.16 97.1% 0+0k 0+0io 0pf+0w