Mon Oct 10 17:04:39 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 17:04:39 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4826 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5122523 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): -18.32300 36.68700 ymin,ymax (A): -30.84500 35.59700 zmin,zma (A): -4.065000 65.43200 x,y,z range (A): 55.01000 66.44200 69.49700 scale (grids/A): 0.5122523 object centre (A): 9.182000 2.375999 30.68350 number of atom coordinates read : 4826 total number of charged atoms : 4579 net assigned charge : 7.800042 assigned positive charge : 725.9943 centred at (gu) : 90.35178 90.30633 88.49441 assigned negative charge : -718.1988 centred at (gu) : 90.23396 90.33974 88.46586 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8045 nv = 96 ne = 84 npr = 97265 no. pairs analyzed = 97265 no. exposed pairs = 6185 no. arc points = 42749 no. surface atoms = 2076 nbur = 2750 mkacc time = 0.2300000 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= 286 mr = 4093 m= 2 mr = 7 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 0.4900000 number of dielectric boundary points 4233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4187 ## 612 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 10715 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5888086E-11 1.3489057E-10 midg,1,midg; midg,igrid,midg 1.9600195E-10 2.7423451E-11 1,midg,midg; igrid,midg,midg -1.9510051E-10 4.8636078E-10 gauss-seidel spectral radius is 0.9805158 estimated iterations to convergence 59 setup time was (sec) 0.7300000 now iterating at: 17:04:40 rms-change max change #iterations 6.9046825E-02 9.554150 at 10iterations 4.4527259E-03 0.8114014 at 20iterations 7.6266396E-04 0.1238670 at 30iterations 2.6476721E-04 3.1631470E-02 at 40iterations 1.0506550E-04 1.3265133E-02 at 50iterations finished qdiffx linear iterations at : 17:04:43 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 1.0506550E-04 1.3265133E-02 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 17:04:44 3.649u 0.164s 0:05.45 69.7% 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 Mon Oct 10 2011 at 17:04:45 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4826 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.536757 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): -18.32300 36.68700 ymin,ymax (A): -30.84500 35.59700 zmin,zma (A): -4.065000 65.43200 x,y,z range (A): 55.01000 66.44200 69.49700 scale (grids/A): 1.536757 object centre (A): 9.182000 2.375999 30.68350 number of atom coordinates read : 4826 total number of charged atoms : 4579 net assigned charge : 7.800042 assigned positive charge : 725.9943 centred at (gu) : 91.05395 90.91781 85.48183 assigned negative charge : -718.1988 centred at (gu) : 90.70185 91.01862 85.39761 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 91426 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42749 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26365 mr = 62576 m= 2186 mr = 17051 m= 51 mr = 863 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 39538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 496 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 34368 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) : 0.5122523 object centre at (A) : 9.182000 2.375999 30.68350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1540202E-03 1.8970167E-02 midg,1,midg; midg,igrid,midg 1.9394242E-03 -9.6582966E-03 1,midg,midg; igrid,midg,midg 3.2912949E-04 1.4346678E-02 gauss-seidel spectral radius is 0.9981362 estimated iterations to convergence 184 setup time was (sec) 0.9900000 now iterating at: 17:04:46 rms-change max change #iterations 3.835273 145.6626 at 10iterations 1.575094 50.14574 at 20iterations 0.6506580 20.00536 at 30iterations 0.2687191 9.037365 at 40iterations 0.1105877 3.384041 at 50iterations 4.5828603E-02 1.383181 at 60iterations 1.9009907E-02 0.5999708 at 70iterations 7.9136519E-03 0.2536678 at 80iterations 3.3124250E-03 0.1013336 at 90iterations 1.4246021E-03 4.9329758E-02 at 100iterations 6.4139906E-04 1.9979477E-02 at 110iterations 3.2116406E-04 1.0093689E-02 at 120iterations finished qdiffx linear iterations at : 17:04:53 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 3.2116406E-04 1.0093689E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 17:04:54 8.244u 0.238s 0:09.47 89.4% 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 Mon Oct 10 2011 at 17:04:54 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4826 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.305135 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): -18.32300 36.68700 ymin,ymax (A): -30.84500 35.59700 zmin,zma (A): -4.065000 65.43200 x,y,z range (A): 55.01000 66.44200 69.49700 scale (grids/A): 2.305135 object centre (A): 9.182000 2.375999 30.68350 number of atom coordinates read : 4826 total number of charged atoms : 4579 net assigned charge : 7.800042 assigned positive charge : 725.9943 centred at (gu) : 91.58060 91.37640 83.22247 assigned negative charge : -718.1988 centred at (gu) : 91.05250 91.52798 83.09632 start vw surface at 0.2500000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 213184 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42749 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 95131 mr = 154166 m= 23265 mr = 73482 m= 3091 mr = 16066 m= 175 mr = 1681 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.770000 number of dielectric boundary points 89404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 75 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 36520 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) : 1.536757 object centre at (A) : 9.182000 2.375999 30.68350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1454415 0.4832757 midg,1,midg; midg,igrid,midg -0.1054550 -0.2550552 1,midg,midg; igrid,midg,midg -1.6164961E-03 0.2233958 gauss-seidel spectral radius is 0.9991738 estimated iterations to convergence 275 setup time was (sec) 2.100000 now iterating at: 17:04:57 rms-change max change #iterations 10.47130 249.7745 at 10iterations 6.068391 170.5269 at 20iterations 3.483238 101.9337 at 30iterations 1.986178 44.03077 at 40iterations 1.127117 26.84687 at 50iterations 0.6374052 14.76297 at 60iterations 0.3586169 9.810731 at 70iterations 0.2014057 4.071324 at 80iterations 0.1132285 2.161228 at 90iterations 6.3332461E-02 1.217676 at 100iterations 3.5497785E-02 0.6791592 at 110iterations 1.9866943E-02 0.4116411 at 120iterations 1.1096319E-02 0.2210732 at 130iterations 6.2217345E-03 0.1196165 at 140iterations 3.4725252E-03 6.4923644E-02 at 150iterations 1.9419016E-03 3.8090706E-02 at 160iterations 1.0874366E-03 2.0010710E-02 at 170iterations 6.0970045E-04 1.2510300E-02 at 180iterations finished qdiffx linear iterations at : 17:05:08 total time elapsed so far: 13.78000 # loops : 180 mean,max change (kT/e) : 6.0970045E-04 1.2510300E-02 energy calculations done at 13.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.97000 DelPhi exited at 17:05:10 13.968u 0.230s 0:15.38 92.2% 0+0k 0+0io 0pf+0w