Tue Nov 22 14:09:54 PST 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 Nov 22 2011 at 14:09:59 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6022466 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): -9.191999 49.92000 ymin,ymax (A): -18.68400 21.76500 zmin,zma (A): -7.692000 34.50700 x,y,z range (A): 59.11200 40.44900 42.19900 scale (grids/A): 0.6022466 object centre (A): 20.36400 1.540500 13.40750 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000013 assigned positive charge : 288.6020 centred at (gu) : 89.92439 89.81464 89.49390 assigned negative charge : -283.6024 centred at (gu) : 89.89476 89.90181 89.36475 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4854 nv = 96 ne = 84 npr = 39734 no. pairs analyzed = 39734 no. exposed pairs = 2469 no. arc points = 17383 no. surface atoms = 849 nbur = 1117 mkacc time = 7.0000008E-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 = 1.456000 m= 231 mr = 2644 m= 0 mr = 17 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1762 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 5879 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6154792E-09 5.3206266E-09 midg,1,midg; midg,igrid,midg 4.9965649E-09 -1.7951905E-10 1,midg,midg; igrid,midg,midg 1.4990298E-09 3.1163998E-09 gauss-seidel spectral radius is 0.9856778 estimated iterations to convergence 69 setup time was (sec) 0.3500000 now iterating at: 14:10:02 rms-change max change #iterations 9.4267122E-02 15.64471 at 10iterations 8.1760939E-03 1.577148 at 20iterations 6.8885367E-04 0.1176376 at 30iterations 5.7142657E-05 1.1642456E-02 at 40iterations 4.9861264E-06 9.4604492E-04 at 50iterations finished qdiffx linear iterations at : 14:10:12 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 4.9861264E-06 9.4604492E-04 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 14:10:14 3.560u 0.231s 0:15.73 24.0% 0+0k 0+0io 3pf+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 Nov 22 2011 at 14:10:18 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.806740 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): -9.191999 49.92000 ymin,ymax (A): -18.68400 21.76500 zmin,zma (A): -7.692000 34.50700 x,y,z range (A): 59.11200 40.44900 42.19900 scale (grids/A): 1.806740 object centre (A): 20.36400 1.540500 13.40750 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000013 assigned positive charge : 288.6020 centred at (gu) : 89.77303 89.44421 88.48155 assigned negative charge : -283.6024 centred at (gu) : 89.68463 89.70564 88.09437 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 52445 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17383 grid for indexing accessible points = 1.400000 m= 17779 mr = 35728 m= 2196 mr = 13147 m= 80 mr = 1269 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 595 time to turn everything in is 0.2800000 number of dielectric boundary points 22339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 14298 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) : 0.6022466 object centre at (A) : 20.36400 1.540500 13.40750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5308926E-03 1.0680571E-02 midg,1,midg; midg,igrid,midg 7.5474470E-03 2.1144550E-03 1,midg,midg; igrid,midg,midg 2.7517322E-02 3.3765730E-02 gauss-seidel spectral radius is 0.9984111 estimated iterations to convergence 199 setup time was (sec) 0.5200000 now iterating at: 14:10:23 rms-change max change #iterations 3.238154 199.5554 at 10iterations 1.429414 54.56676 at 20iterations 0.6302677 23.93476 at 30iterations 0.2772826 10.43212 at 40iterations 0.1222087 4.762044 at 50iterations 5.4104801E-02 2.138168 at 60iterations 2.3799622E-02 0.9077988 at 70iterations 1.0512991E-02 0.4261090 at 80iterations 4.6343626E-03 0.1839981 at 90iterations 2.0400125E-03 7.8414917E-02 at 100iterations 9.0017624E-04 3.2376766E-02 at 110iterations 3.9663148E-04 1.4204979E-02 at 120iterations finished qdiffx linear iterations at : 14:10:48 total time elapsed so far: 8.820000 # loops : 120 mean,max change (kT/e) : 3.9663148E-04 1.4204979E-02 energy calculations done at 8.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.950000 DelPhi exited at 14:10:49 8.950u 0.240s 0:31.59 29.0% 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 Nov 22 2011 at 14:10:51 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.710110 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): -9.191999 49.92000 ymin,ymax (A): -18.68400 21.76500 zmin,zma (A): -7.692000 34.50700 x,y,z range (A): 59.11200 40.44900 42.19900 scale (grids/A): 2.710110 object centre (A): 20.36400 1.540500 13.40750 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000013 assigned positive charge : 288.6020 centred at (gu) : 89.65957 89.16615 87.72232 assigned negative charge : -283.6024 centred at (gu) : 89.52700 89.55858 87.14159 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 121449 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17383 grid for indexing accessible points = 1.400000 m= 59166 mr = 86819 m= 19416 mr = 48469 m= 3697 mr = 15553 m= 358 mr = 2664 m= 18 mr = 214 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1979 time to turn everything in is 0.7000000 number of dielectric boundary points 50386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 14669 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) : 1.806740 object centre at (A) : 20.36400 1.540500 13.40750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5167093E-02 8.8800311E-02 midg,1,midg; midg,igrid,midg 5.4501083E-02 5.6804147E-02 1,midg,midg; igrid,midg,midg 0.3278221 0.3955717 gauss-seidel spectral radius is 0.9991776 estimated iterations to convergence 275 setup time was (sec) 0.9500000 now iterating at: 14:10:57 rms-change max change #iterations 7.829627 304.6709 at 10iterations 4.436341 118.1100 at 20iterations 2.489679 57.44447 at 30iterations 1.388342 31.70590 at 40iterations 0.7752363 18.89958 at 50iterations 0.4327926 10.17475 at 60iterations 0.2414558 5.988255 at 70iterations 0.1343089 2.987333 at 80iterations 7.4764207E-02 1.592454 at 90iterations 4.1613501E-02 0.9899740 at 100iterations 2.3152728E-02 0.5298424 at 110iterations 1.2903057E-02 0.2963858 at 120iterations 7.1556424E-03 0.1661530 at 130iterations 3.9773965E-03 8.6719513E-02 at 140iterations 2.2160499E-03 4.8095703E-02 at 150iterations 1.2287500E-03 2.7655602E-02 at 160iterations 6.8519829E-04 1.4421463E-02 at 170iterations 3.8199007E-04 7.9951286E-03 at 180iterations finished qdiffx linear iterations at : 14:11:36 total time elapsed so far: 13.65000 # loops : 180 mean,max change (kT/e) : 3.8199007E-04 7.9951286E-03 energy calculations done at 13.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.78000 DelPhi exited at 14:11:38 13.782u 0.233s 0:46.87 29.8% 0+0k 0+0io 0pf+0w