Tue Oct 11 03:43:59 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 Tue Oct 11 2011 at 03:43:59 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3077 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 234 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6591128 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): -11.63700 36.94700 ymin,ymax (A): -27.12800 21.48200 zmin,zma (A): -8.409000 45.60300 x,y,z range (A): 48.58400 48.61000 54.01200 scale (grids/A): 0.6591128 object centre (A): 12.65500 -2.823000 18.59700 number of atom coordinates read : 3077 total number of charged atoms : 2671 net assigned charge : -1.298981 assigned positive charge : 427.0937 centred at (gu) : 90.07300 90.68042 91.38094 assigned negative charge : -428.3933 centred at (gu) : 89.80219 90.61826 91.32387 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8273 nv = 96 ne = 84 npr = 57754 no. pairs analyzed = 57754 no. exposed pairs = 3341 no. arc points = 23437 no. surface atoms = 1116 nbur = 1961 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 467 mr = 4829 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.3500000 number of dielectric boundary points 3859 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2303 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 9742 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1768242E-08 1.1673969E-08 midg,1,midg; midg,igrid,midg -1.4561395E-08 1.1245997E-08 1,midg,midg; igrid,midg,midg -6.1893665E-08 5.3442388E-08 gauss-seidel spectral radius is 0.9880874 estimated iterations to convergence 75 setup time was (sec) 0.7600000 now iterating at: 03:44:00 rms-change max change #iterations 0.1766555 21.95704 at 10iterations 1.9428328E-02 2.489964 at 20iterations 2.2218793E-03 0.3059692 at 30iterations 3.6147365E-04 4.0077209E-02 at 40iterations 9.3186994E-05 9.8991394E-03 at 50iterations finished qdiffx linear iterations at : 03:44:05 total time elapsed so far: 5.570000 # loops : 50 mean,max change (kT/e) : 9.3186994E-05 9.8991394E-03 energy calculations done at 5.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.740000 DelPhi exited at 03:44:06 5.745u 0.450s 0:07.05 87.8% 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 Oct 11 2011 at 03:44:06 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3077 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 234 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.977338 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): -11.63700 36.94700 ymin,ymax (A): -27.12800 21.48200 zmin,zma (A): -8.409000 45.60300 x,y,z range (A): 48.58400 48.61000 54.01200 scale (grids/A): 1.977338 object centre (A): 12.65500 -2.823000 18.59700 number of atom coordinates read : 3077 total number of charged atoms : 2671 net assigned charge : -1.298981 assigned positive charge : 427.0937 centred at (gu) : 90.21841 92.04083 94.14217 assigned negative charge : -428.3933 centred at (gu) : 89.40625 91.85458 93.97117 start vw surface at 0.1300000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 88890 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23437 grid for indexing accessible points = 1.400000 m= 34585 mr = 63812 m= 5885 mr = 26465 m= 373 mr = 3798 m= 8 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 183 time to turn everything in is 0.7600000 number of dielectric boundary points 35519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 21064 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) : 0.6591128 object centre at (A) : 12.65500 -2.823000 18.59700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9871093E-02 7.8995675E-03 midg,1,midg; midg,igrid,midg -1.3647016E-02 -4.6091108E-03 1,midg,midg; igrid,midg,midg -1.6346820E-02 6.7426972E-02 gauss-seidel spectral radius is 0.9987498 estimated iterations to convergence 224 setup time was (sec) 1.140000 now iterating at: 03:44:08 rms-change max change #iterations 4.851945 224.7715 at 10iterations 2.356358 84.20473 at 20iterations 1.142644 36.44214 at 30iterations 0.5548176 17.76570 at 40iterations 0.2703333 7.652382 at 50iterations 0.1306951 4.034367 at 60iterations 6.3382894E-02 1.825981 at 70iterations 3.0764535E-02 0.8874474 at 80iterations 1.4972072E-02 0.4100149 at 90iterations 7.3248157E-03 0.2036934 at 100iterations 3.6005138E-03 0.1067042 at 110iterations 1.7930388E-03 5.5363715E-02 at 120iterations finished qdiffx linear iterations at : 03:44:21 total time elapsed so far: 13.42000 # loops : 120 mean,max change (kT/e) : 1.7930388E-03 5.5363715E-02 energy calculations done at 13.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.59000 DelPhi exited at 03:44:22 13.591u 0.636s 0:15.38 92.4% 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 Tue Oct 11 2011 at 03:44:22 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3077 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 234 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.966007 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): -11.63700 36.94700 ymin,ymax (A): -27.12800 21.48200 zmin,zma (A): -8.409000 45.60300 x,y,z range (A): 48.58400 48.61000 54.01200 scale (grids/A): 2.966007 object centre (A): 12.65500 -2.823000 18.59700 number of atom coordinates read : 3077 total number of charged atoms : 2671 net assigned charge : -1.298981 assigned positive charge : 427.0937 centred at (gu) : 90.32740 93.06122 96.21305 assigned negative charge : -428.3933 centred at (gu) : 89.10916 92.78181 95.95670 start vw surface at 0.1200000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 205348 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23437 grid for indexing accessible points = 1.400000 m= 109985 mr = 153506 m= 42456 mr = 92320 m= 10784 mr = 35032 m= 1559 mr = 8147 m= 118 mr = 1022 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 671 time to turn everything in is 1.980000 number of dielectric boundary points 80156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 21357 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) : 1.977338 object centre at (A) : 12.65500 -2.823000 18.59700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1917743 0.2744894 midg,1,midg; midg,igrid,midg -0.1684155 4.2519502E-02 1,midg,midg; igrid,midg,midg -6.3470863E-02 0.6000603 gauss-seidel spectral radius is 0.9992846 estimated iterations to convergence 295 setup time was (sec) 2.330000 now iterating at: 03:44:25 rms-change max change #iterations 11.13539 425.2075 at 10iterations 6.558392 158.1573 at 20iterations 3.848588 83.49105 at 30iterations 2.257204 44.81397 at 40iterations 1.322715 23.20182 at 50iterations 0.7722242 14.82674 at 60iterations 0.4511414 8.651323 at 70iterations 0.2631567 4.572521 at 80iterations 0.1534162 2.816539 at 90iterations 8.9297369E-02 1.508528 at 100iterations 5.2054610E-02 0.8671112 at 110iterations 3.0352253E-02 0.6249466 at 120iterations 1.7667279E-02 0.2936783 at 130iterations 1.0295741E-02 0.1730356 at 140iterations 6.0312753E-03 9.9208832E-02 at 150iterations 3.5478168E-03 6.4289093E-02 at 160iterations 2.0996665E-03 3.6266327E-02 at 170iterations 1.2577679E-03 2.1566391E-02 at 180iterations finished qdiffx linear iterations at : 03:44:43 total time elapsed so far: 19.89000 # loops : 180 mean,max change (kT/e) : 1.2577679E-03 2.1566391E-02 energy calculations done at 19.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.07000 DelPhi exited at 03:44:43 20.071u 0.533s 0:21.42 96.1% 0+0k 0+0io 0pf+0w