Mon Oct 10 09:45:55 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 Mon Oct 10 2011 at 09:45:55 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2872 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5689901 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): -17.68600 34.16500 ymin,ymax (A): -59.65200 -0.9940001 zmin,zma (A): -2.094000 60.47300 x,y,z range (A): 51.85100 58.65800 62.56700 scale (grids/A): 0.5689901 object centre (A): 8.239499 -30.32300 29.18950 number of atom coordinates read : 2872 total number of charged atoms : 2720 net assigned charge : 8.000026 assigned positive charge : 421.2508 centred at (gu) : 88.54442 88.07154 88.15089 assigned negative charge : -413.2513 centred at (gu) : 88.66129 87.89192 87.98785 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6292 nv = 96 ne = 84 npr = 55280 no. pairs analyzed = 55280 no. exposed pairs = 4417 no. arc points = 32673 no. surface atoms = 1463 nbur = 1409 mkacc time = 0.1300000 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= 298 mr = 2611 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3968 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3162 ## 337 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7192963E-09 2.2483517E-09 midg,1,midg; midg,igrid,midg -2.1421287E-09 2.3467759E-09 1,midg,midg; igrid,midg,midg 4.0474233E-09 -2.6794891E-10 gauss-seidel spectral radius is 0.9840784 estimated iterations to convergence 65 setup time was (sec) 0.5800000 now iterating at: 09:45:56 rms-change max change #iterations 8.7695703E-02 14.63231 at 10iterations 6.4856983E-03 1.236006 at 20iterations 5.1864760E-04 8.8977814E-02 at 30iterations 5.5725923E-05 1.0864258E-02 at 40iterations 9.3688250E-06 1.9798279E-03 at 50iterations finished qdiffx linear iterations at : 09:45:58 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 9.3688250E-06 1.9798279E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 09:45:59 3.385u 0.122s 0:03.91 89.5% 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 09:45:59 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2872 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.706970 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): -17.68600 34.16500 ymin,ymax (A): -59.65200 -0.9940001 zmin,zma (A): -2.094000 60.47300 x,y,z range (A): 51.85100 58.65800 62.56700 scale (grids/A): 1.706970 object centre (A): 8.239499 -30.32300 29.18950 number of atom coordinates read : 2872 total number of charged atoms : 2720 net assigned charge : 8.000026 assigned positive charge : 421.2508 centred at (gu) : 85.63262 84.21378 84.45236 assigned negative charge : -413.2513 centred at (gu) : 85.98386 83.67554 83.96309 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 67045 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32673 grid for indexing accessible points = 1.400000 m= 20244 mr = 39561 m= 2517 mr = 12232 m= 92 mr = 1083 m= 0 mr = 6 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 37016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 298 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 21074 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) : 0.5689901 object centre at (A) : 8.239499 -30.32300 29.18950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1960140E-02 8.9515392E-03 midg,1,midg; midg,igrid,midg 2.0207683E-02 2.9726125E-02 1,midg,midg; igrid,midg,midg 1.2237244E-02 3.0880037E-03 gauss-seidel spectral radius is 0.9983621 estimated iterations to convergence 196 setup time was (sec) 0.8600000 now iterating at: 09:46:00 rms-change max change #iterations 3.521315 150.3338 at 10iterations 1.518923 63.22992 at 20iterations 0.6566146 25.62507 at 30iterations 0.2858238 10.14911 at 40iterations 0.1235031 4.601705 at 50iterations 5.3704657E-02 2.097291 at 60iterations 2.3219874E-02 0.8850708 at 70iterations 1.0073957E-02 0.3670015 at 80iterations 4.3920404E-03 0.1536322 at 90iterations 1.9046998E-03 7.7245235E-02 at 100iterations 8.2773052E-04 3.2630920E-02 at 110iterations 3.6080307E-04 1.3114929E-02 at 120iterations finished qdiffx linear iterations at : 09:46:07 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 3.6080307E-04 1.3114929E-02 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 09:46:08 8.453u 0.261s 0:09.17 94.9% 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 09:46:08 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2872 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.560455 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): -17.68600 34.16500 ymin,ymax (A): -59.65200 -0.9940001 zmin,zma (A): -2.094000 60.47300 x,y,z range (A): 51.85100 58.65800 62.56700 scale (grids/A): 2.560455 object centre (A): 8.239499 -30.32300 29.18950 number of atom coordinates read : 2872 total number of charged atoms : 2720 net assigned charge : 8.000026 assigned positive charge : 421.2508 centred at (gu) : 83.44891 81.32066 81.67837 assigned negative charge : -413.2513 centred at (gu) : 83.97576 80.51312 80.94455 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 155054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32673 grid for indexing accessible points = 1.400000 m= 66694 mr = 98285 m= 20691 mr = 48237 m= 3861 mr = 14301 m= 320 mr = 2261 m= 4 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 83404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 21749 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) : 1.706970 object centre at (A) : 8.239499 -30.32300 29.18950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3362831 5.5916049E-02 midg,1,midg; midg,igrid,midg 0.4401163 0.3825095 1,midg,midg; igrid,midg,midg 7.2079316E-02 5.1215056E-02 gauss-seidel spectral radius is 0.9992101 estimated iterations to convergence 281 setup time was (sec) 1.660000 now iterating at: 09:46:10 rms-change max change #iterations 9.221452 339.5936 at 10iterations 5.438081 147.4332 at 20iterations 3.159407 83.42693 at 30iterations 1.822384 44.00458 at 40iterations 1.044645 26.46892 at 50iterations 0.5975205 13.68142 at 60iterations 0.3400720 7.680071 at 70iterations 0.1932331 4.572472 at 80iterations 0.1097746 2.455801 at 90iterations 6.1992608E-02 1.456093 at 100iterations 3.5232663E-02 0.8503046 at 110iterations 1.9888243E-02 0.4214592 at 120iterations 1.1219623E-02 0.2442055 at 130iterations 6.3451831E-03 0.1298714 at 140iterations 3.5791239E-03 6.9472790E-02 at 150iterations 2.0178286E-03 4.4419765E-02 at 160iterations 1.1386975E-03 2.4534225E-02 at 170iterations 6.4287224E-04 1.2748718E-02 at 180iterations finished qdiffx linear iterations at : 09:46:22 total time elapsed so far: 13.28000 # loops : 180 mean,max change (kT/e) : 6.4287224E-04 1.2748718E-02 energy calculations done at 13.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.47000 DelPhi exited at 09:46:22 13.474u 0.316s 0:14.15 97.3% 0+0k 0+0io 0pf+0w