Tue Oct 11 03:22:52 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 Tue Oct 11 2011 at 03:22:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2521 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: 0.5596164 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): -21.77000 27.70800 ymin,ymax (A): -2.354000 52.73800 zmin,zma (A): -26.32000 37.29500 x,y,z range (A): 49.47800 55.09200 63.61500 scale (grids/A): 0.5596164 object centre (A): 2.969000 25.19200 5.487501 number of atom coordinates read : 2521 total number of charged atoms : 2372 net assigned charge : -0.4999916 assigned positive charge : 375.1519 centred at (gu) : 90.84711 92.87096 87.88172 assigned negative charge : -375.6529 centred at (gu) : 90.86808 92.75027 87.90060 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5209 nv = 96 ne = 84 npr = 49359 no. pairs analyzed = 49359 no. exposed pairs = 3298 no. arc points = 24433 no. surface atoms = 1099 nbur = 1422 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 = 1.512000 m= 206 mr = 2555 m= 0 mr = 16 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.1900000 number of dielectric boundary points 2844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2451 ## 323 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6666 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4237198E-10 -1.5641612E-10 midg,1,midg; midg,igrid,midg -6.0046429E-10 2.0390920E-09 1,midg,midg; igrid,midg,midg 8.2138921E-11 -3.4403239E-10 gauss-seidel spectral radius is 0.9834996 estimated iterations to convergence 64 setup time was (sec) 0.3800000 now iterating at: 03:22:53 rms-change max change #iterations 7.3585294E-02 13.66070 at 10iterations 5.0957412E-03 0.8781624 at 20iterations 3.7116770E-04 6.0615063E-02 at 30iterations 2.5633561E-05 4.2991638E-03 at 40iterations 1.8939166E-06 2.8610229E-04 at 50iterations finished qdiffx linear iterations at : 03:22:55 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.8939166E-06 2.8610229E-04 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 03:22:56 3.341u 0.154s 0:03.83 91.1% 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 Tue Oct 11 2011 at 03:22:56 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 = 2521 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: 1.678849 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): -21.77000 27.70800 ymin,ymax (A): -2.354000 52.73800 zmin,zma (A): -26.32000 37.29500 x,y,z range (A): 49.47800 55.09200 63.61500 scale (grids/A): 1.678849 object centre (A): 2.969000 25.19200 5.487501 number of atom coordinates read : 2521 total number of charged atoms : 2372 net assigned charge : -0.4999916 assigned positive charge : 375.1519 centred at (gu) : 92.54076 98.61248 83.64466 assigned negative charge : -375.6529 centred at (gu) : 92.60413 98.25066 83.70189 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 57298 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24433 grid for indexing accessible points = 1.400000 m= 17013 mr = 37213 m= 1813 mr = 11551 m= 61 mr = 910 m= 0 mr = 8 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 319 time to turn everything in is 0.2900000 number of dielectric boundary points 26503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 253 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 18252 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) : 0.5596164 object centre at (A) : 2.969000 25.19200 5.487501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6349324E-03 -1.6965717E-02 midg,1,midg; midg,igrid,midg -4.9637659E-03 1.5712544E-02 1,midg,midg; igrid,midg,midg 9.4330945E-04 -8.8814110E-04 gauss-seidel spectral radius is 0.9982320 estimated iterations to convergence 189 setup time was (sec) 0.5100000 now iterating at: 03:22:57 rms-change max change #iterations 3.178956 161.3311 at 10iterations 1.327510 61.33453 at 20iterations 0.5627477 26.11123 at 30iterations 0.2350304 8.792099 at 40iterations 9.9425845E-02 3.555378 at 50iterations 4.1696969E-02 1.757664 at 60iterations 1.7571628E-02 0.7168446 at 70iterations 7.4046152E-03 0.2737465 at 80iterations 3.1279465E-03 0.1129408 at 90iterations 1.3160818E-03 5.4225922E-02 at 100iterations 5.5737997E-04 2.1071434E-02 at 110iterations 2.3505976E-04 9.5252991E-03 at 120iterations finished qdiffx linear iterations at : 03:23:04 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 2.3505976E-04 9.5252991E-03 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 03:23:04 7.529u 0.171s 0:07.99 96.2% 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 03:23:04 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 = 2521 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: 2.518274 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): -21.77000 27.70800 ymin,ymax (A): -2.354000 52.73800 zmin,zma (A): -26.32000 37.29500 x,y,z range (A): 49.47800 55.09200 63.61500 scale (grids/A): 2.518274 object centre (A): 2.969000 25.19200 5.487501 number of atom coordinates read : 2521 total number of charged atoms : 2372 net assigned charge : -0.4999916 assigned positive charge : 375.1519 centred at (gu) : 93.81101 102.9186 80.46692 assigned negative charge : -375.6529 centred at (gu) : 93.90633 102.3760 80.55278 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 133180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24433 grid for indexing accessible points = 1.400000 m= 59027 mr = 91675 m= 17011 mr = 46061 m= 2783 mr = 12764 m= 209 mr = 1845 m= 4 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 983 time to turn everything in is 0.6700000 number of dielectric boundary points 59777 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 18968 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) : 1.678849 object centre at (A) : 2.969000 25.19200 5.487501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1262693 -0.2472349 midg,1,midg; midg,igrid,midg -5.8671299E-02 0.1966511 1,midg,midg; igrid,midg,midg 2.3796616E-02 -8.0171237E-03 gauss-seidel spectral radius is 0.9991364 estimated iterations to convergence 269 setup time was (sec) 0.9000000 now iterating at: 03:23:05 rms-change max change #iterations 8.143977 295.5228 at 10iterations 4.530659 130.9686 at 20iterations 2.513716 62.18709 at 30iterations 1.387977 31.82675 at 40iterations 0.7677949 19.13471 at 50iterations 0.4227496 10.80068 at 60iterations 0.2330143 5.400772 at 70iterations 0.1282623 3.390228 at 80iterations 7.0392489E-02 1.501460 at 90iterations 3.8700268E-02 0.9105568 at 100iterations 2.1260148E-02 0.4543571 at 110iterations 1.1656453E-02 0.2752686 at 120iterations 6.4165001E-03 0.1361198 at 130iterations 3.5059969E-03 8.2265854E-02 at 140iterations 1.9253606E-03 4.3259054E-02 at 150iterations 1.0589233E-03 2.4467468E-02 at 160iterations 5.8148470E-04 1.2157440E-02 at 170iterations 3.1805717E-04 6.9084167E-03 at 180iterations finished qdiffx linear iterations at : 03:23:16 total time elapsed so far: 11.77000 # loops : 180 mean,max change (kT/e) : 3.1805717E-04 6.9084167E-03 energy calculations done at 11.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 03:23:16 11.912u 0.204s 0:12.39 97.7% 0+0k 0+0io 0pf+0w