Sat Oct 8 13:02:11 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+sph.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 = amb.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 Sat Oct 8 2011 at 13:02:11 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2944 !!! WARNING: GLU 326 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.6400691 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): -24.90900 25.62800 ymin,ymax (A): -26.11200 25.36300 zmin,zma (A): -8.202000 47.41700 x,y,z range (A): 50.53700 51.47500 55.61900 scale (grids/A): 0.6400691 object centre (A): 0.3594999 -0.3745003 19.60750 number of atom coordinates read : 2944 total number of charged atoms : 2798 net assigned charge : 4.226040 assigned positive charge : 436.2382 centred at (gu) : 91.42191 89.95746 91.44765 assigned negative charge : -432.0131 centred at (gu) : 91.54189 89.98447 91.62564 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8177 nv = 96 ne = 84 npr = 59696 no. pairs analyzed = 59696 no. exposed pairs = 3586 no. arc points = 25161 no. surface atoms = 1207 nbur = 1737 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 4668 m= 3 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 81 time to turn everything in is 0.3400000 number of dielectric boundary points 3897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2469 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9781 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1563149E-08 -2.3116376E-08 midg,1,midg; midg,igrid,midg 1.0370709E-08 3.2589980E-09 1,midg,midg; igrid,midg,midg 1.6335727E-08 -1.2369345E-08 gauss-seidel spectral radius is 0.9873841 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 13:02:12 rms-change max change #iterations 0.1563396 21.88763 at 10iterations 1.5895108E-02 2.308176 at 20iterations 2.1306539E-03 0.3232155 at 30iterations 6.9308450E-04 0.1335831 at 40iterations 3.2508120E-04 6.3709259E-02 at 50iterations finished qdiffx linear iterations at : 13:02:14 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 3.2508120E-04 6.3709259E-02 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 13:02:15 3.152u 0.123s 0:03.56 91.8% 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 Sat Oct 8 2011 at 13:02:15 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2944 !!! WARNING: GLU 326 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.920207 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): -24.90900 25.62800 ymin,ymax (A): -26.11200 25.36300 zmin,zma (A): -8.202000 47.41700 x,y,z range (A): 50.53700 51.47500 55.61900 scale (grids/A): 1.920207 object centre (A): 0.3594999 -0.3745003 19.60750 number of atom coordinates read : 2944 total number of charged atoms : 2798 net assigned charge : 4.226040 assigned positive charge : 436.2382 centred at (gu) : 94.26482 89.87142 94.34225 assigned negative charge : -432.0131 centred at (gu) : 94.62531 89.95313 94.87617 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 88228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25161 grid for indexing accessible points = 1.400000 m= 33229 mr = 62656 m= 5349 mr = 25109 m= 303 mr = 3382 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 4613 time to turn everything in is 0.6000000 number of dielectric boundary points 35892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 22034 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) : 0.6400691 object centre at (A) : 0.3594999 -0.3745003 19.60750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7996030E-02 1.7821506E-03 midg,1,midg; midg,igrid,midg 2.0674005E-02 1.5667176E-02 1,midg,midg; igrid,midg,midg 1.2444135E-02 -7.3063147E-04 gauss-seidel spectral radius is 0.9986884 estimated iterations to convergence 219 setup time was (sec) 0.8600000 now iterating at: 13:02:16 rms-change max change #iterations 4.567129 186.9019 at 10iterations 2.164506 77.90176 at 20iterations 1.034417 34.44794 at 30iterations 0.4898996 14.73698 at 40iterations 0.2334682 6.890671 at 50iterations 0.1109248 3.319691 at 60iterations 5.2899171E-02 1.518194 at 70iterations 2.5344526E-02 0.7486324 at 80iterations 1.2215474E-02 0.3696957 at 90iterations 6.0046837E-03 0.1856966 at 100iterations 3.1290438E-03 0.1049271 at 110iterations 1.7818904E-03 6.5856934E-02 at 120iterations finished qdiffx linear iterations at : 13:02:22 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 1.7818904E-03 6.5856934E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 13:02:22 7.079u 0.171s 0:07.55 95.8% 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 Sat Oct 8 2011 at 13:02:22 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2944 !!! WARNING: GLU 326 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.880311 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): -24.90900 25.62800 ymin,ymax (A): -26.11200 25.36300 zmin,zma (A): -8.202000 47.41700 x,y,z range (A): 50.53700 51.47500 55.61900 scale (grids/A): 2.880311 object centre (A): 0.3594999 -0.3745003 19.60750 number of atom coordinates read : 2944 total number of charged atoms : 2798 net assigned charge : 4.226040 assigned positive charge : 436.2382 centred at (gu) : 96.39725 89.80690 96.51324 assigned negative charge : -432.0131 centred at (gu) : 96.93787 89.92953 97.31422 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 203679 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25161 grid for indexing accessible points = 1.400000 m= 106726 mr = 150975 m= 39955 mr = 88791 m= 9736 mr = 32595 m= 1287 mr = 7249 m= 76 mr = 775 m= 0 mr = 18 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 15148 time to turn everything in is 1.520000 number of dielectric boundary points 81056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 22372 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) : 1.920207 object centre at (A) : 0.3594999 -0.3745003 19.60750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1386665 0.1849428 midg,1,midg; midg,igrid,midg 0.2332760 0.2974038 1,midg,midg; igrid,midg,midg 3.8161717E-02 6.7020670E-02 gauss-seidel spectral radius is 0.9992788 estimated iterations to convergence 294 setup time was (sec) 1.800000 now iterating at: 13:02:24 rms-change max change #iterations 10.68339 405.5309 at 10iterations 6.285348 136.2888 at 20iterations 3.669876 74.56217 at 30iterations 2.143380 38.76900 at 40iterations 1.247790 26.63072 at 50iterations 0.7262886 12.57581 at 60iterations 0.4229980 7.092697 at 70iterations 0.2458604 4.289795 at 80iterations 0.1425988 2.407706 at 90iterations 8.2700849E-02 1.367639 at 100iterations 4.8133016E-02 0.8373251 at 110iterations 2.7970461E-02 0.5372391 at 120iterations 1.6326144E-02 0.2922802 at 130iterations 9.6124057E-03 0.1783180 at 140iterations 5.7302807E-03 0.1129522 at 150iterations 3.5406384E-03 7.2021484E-02 at 160iterations 2.3086730E-03 5.2341461E-02 at 170iterations 1.6307934E-03 3.8002014E-02 at 180iterations finished qdiffx linear iterations at : 13:02:34 total time elapsed so far: 11.44000 # loops : 180 mean,max change (kT/e) : 1.6307934E-03 3.8002014E-02 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.61000 DelPhi exited at 13:02:34 11.616u 0.179s 0:12.07 97.5% 0+0k 0+0io 0pf+0w