Sun Oct 9 08:38:21 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+sph2.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 = amb2.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 08:38:21 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5608 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 0.5459285 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): -42.71100 22.49900 ymin,ymax (A): -13.97600 50.35900 zmin,zma (A): -39.64300 24.71900 x,y,z range (A): 65.21000 64.33500 64.36200 scale (grids/A): 0.5459285 object centre (A): -10.10600 18.19150 -7.462001 number of atom coordinates read : 5608 total number of charged atoms : 5440 net assigned charge : -4.485980 assigned positive charge : 843.4100 centred at (gu) : 90.20000 89.48067 88.97084 assigned negative charge : -847.9026 centred at (gu) : 90.13676 89.38026 88.98018 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 10676 nv = 96 ne = 84 npr = 113523 no. pairs analyzed = 113523 no. exposed pairs = 7117 no. arc points = 49057 no. surface atoms = 2402 nbur = 3206 mkacc time = 0.2400000 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 = 1.568000 m= 445 mr = 5605 m= 4 mr = 20 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 0.5000000 number of dielectric boundary points 5500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4951 ## 646 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 14218 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9778923E-10 -3.0539996E-10 midg,1,midg; midg,igrid,midg -1.7755719E-09 8.5832985E-10 1,midg,midg; igrid,midg,midg -1.0270115E-09 5.4690252E-10 gauss-seidel spectral radius is 0.9829014 estimated iterations to convergence 63 setup time was (sec) 0.7200000 now iterating at: 08:38:22 rms-change max change #iterations 0.1022220 13.66322 at 10iterations 7.2978735E-03 0.8809929 at 20iterations 7.3442003E-04 0.1183472 at 30iterations 1.7882648E-04 3.5697937E-02 at 40iterations 5.9844115E-05 1.2012482E-02 at 50iterations finished qdiffx linear iterations at : 08:38:24 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 5.9844115E-05 1.2012482E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 08:38:25 3.358u 0.165s 0:03.79 92.6% 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 08:38:25 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5608 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.637786 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): -42.71100 22.49900 ymin,ymax (A): -13.97600 50.35900 zmin,zma (A): -39.64300 24.71900 x,y,z range (A): 65.21000 64.33500 64.36200 scale (grids/A): 1.637786 object centre (A): -10.10600 18.19150 -7.462001 number of atom coordinates read : 5608 total number of charged atoms : 5440 net assigned charge : -4.485980 assigned positive charge : 843.4100 centred at (gu) : 90.59828 88.43987 86.91040 assigned negative charge : -847.9026 centred at (gu) : 90.41006 88.14045 86.94029 start vw surface at 0.2100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 118501 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49057 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 37810 mr = 81234 m= 4119 mr = 25953 m= 124 mr = 2014 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 470 time to turn everything in is 0.7800000 number of dielectric boundary points 51351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 544 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 41670 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) : 0.5459285 object centre at (A) : -10.10600 18.19150 -7.462001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6323667E-03 -1.8660026E-02 midg,1,midg; midg,igrid,midg -3.6638789E-02 1.3838680E-02 1,midg,midg; igrid,midg,midg -6.9619222E-03 1.0550263E-02 gauss-seidel spectral radius is 0.9984517 estimated iterations to convergence 202 setup time was (sec) 1.070000 now iterating at: 08:38:26 rms-change max change #iterations 4.877090 197.0261 at 10iterations 2.170578 62.67849 at 20iterations 0.9662830 25.37688 at 30iterations 0.4317424 11.83746 at 40iterations 0.1926463 5.502639 at 50iterations 8.5942321E-02 2.392075 at 60iterations 3.8362261E-02 1.069511 at 70iterations 1.7163299E-02 0.5390043 at 80iterations 7.6950300E-03 0.2108994 at 90iterations 3.4459441E-03 9.4129562E-02 at 100iterations 1.5569434E-03 4.3916702E-02 at 110iterations 7.1225892E-04 2.0353317E-02 at 120iterations finished qdiffx linear iterations at : 08:38:32 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 7.1225892E-04 2.0353317E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 08:38:33 7.714u 0.198s 0:08.19 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 08:38:33 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5608 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.2300000 grid size : 179 scale,in grids/A, set to be: 2.456678 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): -42.71100 22.49900 ymin,ymax (A): -13.97600 50.35900 zmin,zma (A): -39.64300 24.71900 x,y,z range (A): 65.21000 64.33500 64.36200 scale (grids/A): 2.456678 object centre (A): -10.10600 18.19150 -7.462001 number of atom coordinates read : 5608 total number of charged atoms : 5440 net assigned charge : -4.485980 assigned positive charge : 843.4100 centred at (gu) : 90.89694 87.65955 85.36510 assigned negative charge : -847.9026 centred at (gu) : 90.61514 87.21072 85.41042 start vw surface at 0.3000000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 275074 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49057 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 130129 mr = 198951 m= 37910 mr = 102405 m= 6364 mr = 28257 m= 520 mr = 4260 m= 6 mr = 208 m= 0 mr = 0 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 1459 time to turn everything in is 2.010000 number of dielectric boundary points 115922 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 43455 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) : 1.637786 object centre at (A) : -10.10600 18.19150 -7.462001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1919424 -0.2290249 midg,1,midg; midg,igrid,midg -0.6806095 0.2180561 1,midg,midg; igrid,midg,midg -8.2436904E-02 0.3838110 gauss-seidel spectral radius is 0.9992881 estimated iterations to convergence 296 setup time was (sec) 2.310000 now iterating at: 08:38:35 rms-change max change #iterations 12.72386 310.9385 at 10iterations 7.670958 170.4164 at 20iterations 4.595320 90.37884 at 30iterations 2.736519 50.35394 at 40iterations 1.626117 33.76676 at 50iterations 0.9623910 18.06562 at 60iterations 0.5680048 9.950626 at 70iterations 0.3344305 5.807850 at 80iterations 0.1967232 3.246979 at 90iterations 0.1152474 2.064495 at 100iterations 6.7612268E-02 1.125194 at 110iterations 3.9578807E-02 0.6959305 at 120iterations 2.3180086E-02 0.3612022 at 130iterations 1.3552387E-02 0.2082667 at 140iterations 7.9168519E-03 0.1399250 at 150iterations 4.6285433E-03 7.2567940E-02 at 160iterations 2.7012688E-03 4.8973322E-02 at 170iterations 1.5793713E-03 2.3566246E-02 at 180iterations finished qdiffx linear iterations at : 08:38:45 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 1.5793713E-03 2.3566246E-02 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 08:38:46 12.326u 0.189s 0:12.78 97.8% 0+0k 0+0io 0pf+0w