Mon Oct 10 20:17:48 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 20:17:48 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4285 !!! WARNING: HIQ 440 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5513054 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): -3.387000 61.18000 ymin,ymax (A): -12.18800 38.37800 zmin,zma (A): -19.52700 45.04700 x,y,z range (A): 64.56700 50.56600 64.57401 scale (grids/A): 0.5513054 object centre (A): 28.89650 13.09500 12.76000 number of atom coordinates read : 4285 total number of charged atoms : 4132 net assigned charge : -4.485941 assigned positive charge : 645.4840 centred at (gu) : 89.18512 89.94614 90.74976 assigned negative charge : -649.9725 centred at (gu) : 89.22073 90.05521 90.77905 start vw surface at 0.2000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8216 nv = 96 ne = 84 npr = 90596 no. pairs analyzed = 90596 no. exposed pairs = 4890 no. arc points = 32364 no. surface atoms = 1670 nbur = 2615 mkacc time = 0.2600000 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 = 1.540000 m= 368 mr = 4739 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.5100000 number of dielectric boundary points 3816 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3328 ## 402 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 10956 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6219421E-12 -8.3121759E-10 midg,1,midg; midg,igrid,midg 9.4125630E-10 -1.6299501E-09 1,midg,midg; igrid,midg,midg 9.6248731E-11 -6.2916689E-10 gauss-seidel spectral radius is 0.9831200 estimated iterations to convergence 63 setup time was (sec) 0.7800000 now iterating at: 20:17:49 rms-change max change #iterations 9.3395554E-02 13.89461 at 10iterations 7.0453282E-03 1.019485 at 20iterations 1.0954355E-03 0.1381683 at 30iterations 3.7700756E-04 4.7931671E-02 at 40iterations 1.4226603E-04 1.8846512E-02 at 50iterations finished qdiffx linear iterations at : 20:17:53 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 1.4226603E-04 1.8846512E-02 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 20:17:53 4.241u 0.271s 0:04.87 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 Mon Oct 10 2011 at 20:17:53 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4285 !!! WARNING: HIQ 440 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.653916 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): -3.387000 61.18000 ymin,ymax (A): -12.18800 38.37800 zmin,zma (A): -19.52700 45.04700 x,y,z range (A): 64.56700 50.56600 64.57401 scale (grids/A): 1.653916 object centre (A): 28.89650 13.09500 12.76000 number of atom coordinates read : 4285 total number of charged atoms : 4132 net assigned charge : -4.485941 assigned positive charge : 645.4840 centred at (gu) : 87.55414 89.83720 92.24813 assigned negative charge : -649.9725 centred at (gu) : 87.66154 90.16544 92.33661 start vw surface at 0.2100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 92592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32364 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30428 mr = 67275 m= 3542 mr = 22016 m= 114 mr = 1921 m= 0 mr = 18 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1560 time to turn everything in is 0.8300000 number of dielectric boundary points 35446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 346 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 31810 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) : 0.5513054 object centre at (A) : 28.89650 13.09500 12.76000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2286323E-02 -1.3406996E-02 midg,1,midg; midg,igrid,midg 5.6206570E-03 -1.9307304E-02 1,midg,midg; igrid,midg,midg 1.7318187E-02 2.9178746E-02 gauss-seidel spectral radius is 0.9983474 estimated iterations to convergence 195 setup time was (sec) 1.130000 now iterating at: 20:17:55 rms-change max change #iterations 4.200090 179.4019 at 10iterations 1.825601 71.98926 at 20iterations 0.7934724 25.88017 at 30iterations 0.3442602 10.30461 at 40iterations 0.1500196 4.796741 at 50iterations 6.5549590E-02 2.016700 at 60iterations 2.8681526E-02 0.9573622 at 70iterations 1.2646188E-02 0.3716431 at 80iterations 5.6484598E-03 0.2016039 at 90iterations 2.6312708E-03 8.1275940E-02 at 100iterations 1.3122543E-03 3.8909912E-02 at 110iterations 7.2715868E-04 2.1831512E-02 at 120iterations finished qdiffx linear iterations at : 20:18:03 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 7.2715868E-04 2.1831512E-02 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.640000 DelPhi exited at 20:18:04 9.641u 0.285s 0:10.56 93.9% 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 20:18:04 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4285 !!! WARNING: HIQ 440 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.480875 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): -3.387000 61.18000 ymin,ymax (A): -12.18800 38.37800 zmin,zma (A): -19.52700 45.04700 x,y,z range (A): 64.56700 50.56600 64.57401 scale (grids/A): 2.480875 object centre (A): 28.89650 13.09500 12.76000 number of atom coordinates read : 4285 total number of charged atoms : 4132 net assigned charge : -4.485941 assigned positive charge : 645.4840 centred at (gu) : 86.33082 89.75556 93.37183 assigned negative charge : -649.9725 centred at (gu) : 86.49220 90.24801 93.50473 start vw surface at 0.2100000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 215902 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32364 grid for indexing accessible points = 1.400000 m= 105374 mr = 164261 m= 31438 mr = 86051 m= 5785 mr = 24372 m= 487 mr = 4022 m= 7 mr = 248 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 5222 time to turn everything in is 2.010000 number of dielectric boundary points 80039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 33031 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) : 1.653916 object centre at (A) : 28.89650 13.09500 12.76000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5410761 -0.3017996 midg,1,midg; midg,igrid,midg 8.2762383E-02 -0.2550488 1,midg,midg; igrid,midg,midg 0.4164671 0.4795084 gauss-seidel spectral radius is 0.9992109 estimated iterations to convergence 281 setup time was (sec) 2.330000 now iterating at: 20:18:06 rms-change max change #iterations 10.81844 356.6624 at 10iterations 6.243334 144.8122 at 20iterations 3.591199 73.39634 at 30iterations 2.057415 36.40627 at 40iterations 1.173836 21.57832 at 50iterations 0.6686687 13.71933 at 60iterations 0.3805856 6.585466 at 70iterations 0.2159814 3.614874 at 80iterations 0.1222166 2.217389 at 90iterations 6.9483973E-02 1.182785 at 100iterations 3.9423477E-02 0.6541939 at 110iterations 2.2368774E-02 0.3928947 at 120iterations 1.2749574E-02 0.2265320 at 130iterations 7.2581358E-03 0.1221018 at 140iterations 4.1928631E-03 7.6232910E-02 at 150iterations 2.4701415E-03 4.2482376E-02 at 160iterations 1.4968881E-03 2.5081635E-02 at 170iterations 9.5234928E-04 1.6461372E-02 at 180iterations finished qdiffx linear iterations at : 20:18:20 total time elapsed so far: 16.19000 # loops : 180 mean,max change (kT/e) : 9.5234928E-04 1.6461372E-02 energy calculations done at 16.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.36000 DelPhi exited at 20:18:21 16.363u 0.321s 0:17.45 95.5% 0+0k 0+0io 0pf+0w