Tue Oct 11 02:44:19 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 02:44:19 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2749 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: FMN 398 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6673540 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): -22.33300 24.67800 ymin,ymax (A): 10.67000 64.01500 zmin,zma (A): -17.58500 30.16300 x,y,z range (A): 47.01100 53.34500 47.74800 scale (grids/A): 0.6673540 object centre (A): 1.172500 37.34250 6.289000 number of atom coordinates read : 2749 total number of charged atoms : 2611 net assigned charge : 8.906014 assigned positive charge : 423.6164 centred at (gu) : 89.72449 89.86440 90.80745 assigned negative charge : -414.7115 centred at (gu) : 89.87674 89.73184 90.84023 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8246 nv = 96 ne = 84 npr = 55683 no. pairs analyzed = 55683 no. exposed pairs = 3396 no. arc points = 23223 no. surface atoms = 1140 nbur = 1609 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 448 mr = 4689 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 48 time to turn everything in is 0.3900000 number of dielectric boundary points 3954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2204 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9667 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0572892E-08 2.2507985E-08 midg,1,midg; midg,igrid,midg -6.8520647E-09 5.9241945E-08 1,midg,midg; igrid,midg,midg 6.9610124E-08 -1.1032084E-08 gauss-seidel spectral radius is 0.9883740 estimated iterations to convergence 76 setup time was (sec) 0.6800000 now iterating at: 02:44:20 rms-change max change #iterations 0.1837759 22.66479 at 10iterations 2.1014972E-02 3.077187 at 20iterations 3.3384701E-03 0.5828705 at 30iterations 1.0109807E-03 0.2127304 at 40iterations 3.7624940E-04 8.0749512E-02 at 50iterations finished qdiffx linear iterations at : 02:44:23 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 3.7624940E-04 8.0749512E-02 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 02:44:24 4.130u 0.168s 0:04.64 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 02:44:24 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2749 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: FMN 398 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.002062 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): -22.33300 24.67800 ymin,ymax (A): 10.67000 64.01500 zmin,zma (A): -17.58500 30.16300 x,y,z range (A): 47.01100 53.34500 47.74800 scale (grids/A): 2.002062 object centre (A): 1.172500 37.34250 6.289000 number of atom coordinates read : 2749 total number of charged atoms : 2611 net assigned charge : 8.906014 assigned positive charge : 423.6164 centred at (gu) : 89.17285 89.59230 92.42167 assigned negative charge : -414.7115 centred at (gu) : 89.63012 89.19497 92.52044 start vw surface at 0.2000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 89190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23223 grid for indexing accessible points = 1.400000 m= 33789 mr = 63029 m= 5933 mr = 25594 m= 412 mr = 3958 m= 3 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 3550 time to turn everything in is 0.8000000 number of dielectric boundary points 36583 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 20654 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) : 0.6673540 object centre at (A) : 1.172500 37.34250 6.289000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5494394E-02 -2.0004960E-02 midg,1,midg; midg,igrid,midg -1.3658805E-02 7.7929124E-02 1,midg,midg; igrid,midg,midg 7.0609070E-02 2.4031965E-02 gauss-seidel spectral radius is 0.9987775 estimated iterations to convergence 226 setup time was (sec) 1.150000 now iterating at: 02:44:25 rms-change max change #iterations 4.895032 252.8900 at 10iterations 2.385379 77.97070 at 20iterations 1.164729 34.83485 at 30iterations 0.5666654 15.63810 at 40iterations 0.2766210 7.530402 at 50iterations 0.1347066 3.759027 at 60iterations 6.6264011E-02 2.030538 at 70iterations 3.2590877E-02 1.013113 at 80iterations 1.6266823E-02 0.4764328 at 90iterations 8.2758116E-03 0.2674828 at 100iterations 4.3850993E-03 0.1578445 at 110iterations 2.4692211E-03 9.8220825E-02 at 120iterations finished qdiffx linear iterations at : 02:44:33 total time elapsed so far: 9.130000 # loops : 120 mean,max change (kT/e) : 2.4692211E-03 9.8220825E-02 energy calculations done at 9.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.360000 DelPhi exited at 02:44:34 9.360u 0.235s 0:10.15 94.4% 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 02:44:34 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2749 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: FMN 398 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 3.003093 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): -22.33300 24.67800 ymin,ymax (A): 10.67000 64.01500 zmin,zma (A): -17.58500 30.16300 x,y,z range (A): 47.01100 53.34500 47.74800 scale (grids/A): 3.003093 object centre (A): 1.172500 37.34250 6.289000 number of atom coordinates read : 2749 total number of charged atoms : 2611 net assigned charge : 8.906014 assigned positive charge : 423.6164 centred at (gu) : 88.75919 89.38834 93.63231 assigned negative charge : -414.7115 centred at (gu) : 89.44514 88.79225 93.78056 start vw surface at 0.2000000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 205992 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23223 grid for indexing accessible points = 1.400000 m= 107591 mr = 152291 m= 41574 mr = 89355 m= 11016 mr = 34039 m= 1813 mr = 8565 m= 130 mr = 1301 m= 0 mr = 68 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 11646 time to turn everything in is 2.100000 number of dielectric boundary points 82497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 20887 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) : 2.002062 object centre at (A) : 1.172500 37.34250 6.289000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2120414 -0.2437869 midg,1,midg; midg,igrid,midg -0.3398881 1.026819 1,midg,midg; igrid,midg,midg 0.6791066 0.2663672 gauss-seidel spectral radius is 0.9992970 estimated iterations to convergence 298 setup time was (sec) 2.470000 now iterating at: 02:44:37 rms-change max change #iterations 11.18744 461.7896 at 10iterations 6.596682 139.1567 at 20iterations 3.886640 74.66295 at 30iterations 2.283874 43.95095 at 40iterations 1.342548 23.33987 at 50iterations 0.7860307 14.03968 at 60iterations 0.4608589 7.911316 at 70iterations 0.2697145 4.393795 at 80iterations 0.1577516 2.955381 at 90iterations 9.2340931E-02 1.653887 at 100iterations 5.4158099E-02 0.9390106 at 110iterations 3.1769477E-02 0.5372849 at 120iterations 1.8728744E-02 0.3287506 at 130iterations 1.1148740E-02 0.2346268 at 140iterations 6.7812437E-03 0.1477280 at 150iterations 4.2687608E-03 9.2733383E-02 at 160iterations 2.8310011E-03 6.4941406E-02 at 170iterations 1.9986783E-03 5.0155640E-02 at 180iterations finished qdiffx linear iterations at : 02:44:49 total time elapsed so far: 14.84000 # loops : 180 mean,max change (kT/e) : 1.9986783E-03 5.0155640E-02 energy calculations done at 14.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.08000 DelPhi exited at 02:44:50 15.084u 0.228s 0:15.97 95.8% 0+0k 0+0io 0pf+0w