Sun Oct 9 23:48:26 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 23:48:26 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 = 3139 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5948601 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): -29.19000 30.65600 ymin,ymax (A): 7.651000 61.92000 zmin,zma (A): 24.96700 77.31400 x,y,z range (A): 59.84600 54.26900 52.34700 scale (grids/A): 0.5948601 object centre (A): 0.7329998 34.78550 51.14050 number of atom coordinates read : 3139 total number of charged atoms : 2994 net assigned charge : 0.5000064 assigned positive charge : 471.7329 centred at (gu) : 89.77448 89.17538 88.91924 assigned negative charge : -471.2342 centred at (gu) : 89.79675 89.17760 89.04769 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7421 nv = 96 ne = 84 npr = 62466 no. pairs analyzed = 62466 no. exposed pairs = 4126 no. arc points = 29372 no. surface atoms = 1367 nbur = 1772 mkacc time = 0.1100000 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 = 1.456000 m= 368 mr = 3881 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 0.2400000 number of dielectric boundary points 3881 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2939 ## 307 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9345 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2991976E-09 -3.7284997E-09 midg,1,midg; midg,igrid,midg 2.4708585E-10 3.3397625E-11 1,midg,midg; igrid,midg,midg 1.0105226E-09 -6.8210892E-10 gauss-seidel spectral radius is 0.9854277 estimated iterations to convergence 68 setup time was (sec) 0.4400000 now iterating at: 23:48:26 rms-change max change #iterations 0.1145815 18.02101 at 10iterations 9.5285857E-03 1.366062 at 20iterations 7.9019327E-04 0.1139441 at 30iterations 7.0469861E-05 1.0428429E-02 at 40iterations 9.5765008E-06 1.3456345E-03 at 50iterations finished qdiffx linear iterations at : 23:48:29 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 9.5765008E-06 1.3456345E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 23:48:30 3.494u 0.152s 0:03.94 92.3% 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 23:48:30 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 = 3139 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.784580 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): -29.19000 30.65600 ymin,ymax (A): 7.651000 61.92000 zmin,zma (A): 24.96700 77.31400 x,y,z range (A): 59.84600 54.26900 52.34700 scale (grids/A): 1.784580 object centre (A): 0.7329998 34.78550 51.14050 number of atom coordinates read : 3139 total number of charged atoms : 2994 net assigned charge : 0.5000064 assigned positive charge : 471.7329 centred at (gu) : 89.32303 87.52511 86.75701 assigned negative charge : -471.2342 centred at (gu) : 89.38985 87.53236 87.14278 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81109 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29372 grid for indexing accessible points = 1.400000 m= 25985 mr = 54743 m= 3241 mr = 17998 m= 125 mr = 1786 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1520 time to turn everything in is 0.4000000 number of dielectric boundary points 35909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 271 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 23368 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) : 0.5948601 object centre at (A) : 0.7329998 34.78550 51.14050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5815314E-03 -5.6659998E-03 midg,1,midg; midg,igrid,midg 9.6835904E-03 5.8089099E-03 1,midg,midg; igrid,midg,midg 2.1056091E-02 8.5160881E-04 gauss-seidel spectral radius is 0.9985177 estimated iterations to convergence 206 setup time was (sec) 0.6100000 now iterating at: 23:48:31 rms-change max change #iterations 4.150221 170.4848 at 10iterations 1.869854 60.95044 at 20iterations 0.8516731 27.48128 at 30iterations 0.3846904 13.11786 at 40iterations 0.1739694 5.494637 at 50iterations 7.8845978E-02 2.681620 at 60iterations 3.5740770E-02 1.264351 at 70iterations 1.6193721E-02 0.4906693 at 80iterations 7.3394156E-03 0.2367175 at 90iterations 3.3322081E-03 0.1049814 at 100iterations 1.5124305E-03 4.6596050E-02 at 110iterations 6.8799453E-04 2.0233154E-02 at 120iterations finished qdiffx linear iterations at : 23:48:38 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 6.8799453E-04 2.0233154E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 23:48:38 7.956u 0.196s 0:08.46 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 Sun Oct 9 2011 at 23:48:38 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 = 3139 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.676871 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): -29.19000 30.65600 ymin,ymax (A): 7.651000 61.92000 zmin,zma (A): 24.96700 77.31400 x,y,z range (A): 59.84600 54.26900 52.34700 scale (grids/A): 2.676871 object centre (A): 0.7329998 34.78550 51.14050 number of atom coordinates read : 3139 total number of charged atoms : 2994 net assigned charge : 0.5000064 assigned positive charge : 471.7329 centred at (gu) : 88.98434 86.28748 85.13528 assigned negative charge : -471.2342 centred at (gu) : 89.08469 86.29848 85.71417 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 188282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29372 grid for indexing accessible points = 1.400000 m= 88365 mr = 134018 m= 27334 mr = 70014 m= 5306 mr = 20773 m= 555 mr = 3758 m= 19 mr = 327 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 5121 time to turn everything in is 0.9800000 number of dielectric boundary points 80971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 23940 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) : 1.784580 object centre at (A) : 0.7329998 34.78550 51.14050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1377068 -1.5955111E-03 midg,1,midg; midg,igrid,midg 7.7308677E-02 0.1132371 1,midg,midg; igrid,midg,midg 0.3310815 1.3764853E-02 gauss-seidel spectral radius is 0.9992523 estimated iterations to convergence 289 setup time was (sec) 1.220000 now iterating at: 23:48:40 rms-change max change #iterations 10.28631 278.4115 at 10iterations 6.093962 144.8499 at 20iterations 3.583368 87.69621 at 30iterations 2.094421 46.50961 at 40iterations 1.221164 25.70562 at 50iterations 0.7072395 15.43911 at 60iterations 0.4096562 7.567793 at 70iterations 0.2364884 4.755133 at 80iterations 0.1366761 2.762012 at 90iterations 7.8633077E-02 1.460739 at 100iterations 4.5397408E-02 0.8147891 at 110iterations 2.6155338E-02 0.4722672 at 120iterations 1.4969811E-02 0.2730181 at 130iterations 8.6109629E-03 0.1513634 at 140iterations 4.9443506E-03 9.0507507E-02 at 150iterations 2.8402654E-03 6.0971737E-02 at 160iterations 1.6291096E-03 3.0209541E-02 at 170iterations 9.3691895E-04 1.7635345E-02 at 180iterations finished qdiffx linear iterations at : 23:48:51 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 9.3691895E-04 1.7635345E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 23:48:52 12.797u 0.206s 0:13.26 97.9% 0+0k 0+0io 0pf+0w