Sun Oct 9 21:26:10 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 Sun Oct 9 2011 at 21:26:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2571 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6497536 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): -11.90800 38.01800 ymin,ymax (A): -21.99100 32.79900 zmin,zma (A): -11.64300 41.52000 x,y,z range (A): 49.92600 54.79000 53.16300 scale (grids/A): 0.6497536 object centre (A): 13.05500 5.404000 14.93850 number of atom coordinates read : 2571 total number of charged atoms : 2428 net assigned charge : 6.000012 assigned positive charge : 387.8779 centred at (gu) : 90.83468 89.46883 90.09475 assigned negative charge : -381.8787 centred at (gu) : 90.76472 89.36050 90.08371 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7159 nv = 96 ne = 84 npr = 51608 no. pairs analyzed = 51608 no. exposed pairs = 3096 no. arc points = 22000 no. surface atoms = 1054 nbur = 1517 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 372 mr = 3909 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 74 time to turn everything in is 0.2000000 number of dielectric boundary points 3573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2190 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8650 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6795825E-09 1.3415298E-08 midg,1,midg; midg,igrid,midg -5.4932223E-09 2.4578632E-08 1,midg,midg; igrid,midg,midg 9.3775998E-10 2.6056412E-08 gauss-seidel spectral radius is 0.9877241 estimated iterations to convergence 74 setup time was (sec) 0.3900000 now iterating at: 21:26:10 rms-change max change #iterations 0.1510266 22.90567 at 10iterations 1.5590304E-02 2.112370 at 20iterations 1.5884005E-03 0.2474327 at 30iterations 1.6361549E-04 2.1099091E-02 at 40iterations 1.6880664E-05 2.7084351E-03 at 50iterations finished qdiffx linear iterations at : 21:26:13 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.6880664E-05 2.7084351E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 21:26:14 3.442u 0.181s 0:03.89 93.0% 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 Sun Oct 9 2011 at 21:26:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2571 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.949261 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): -11.90800 38.01800 ymin,ymax (A): -21.99100 32.79900 zmin,zma (A): -11.64300 41.52000 x,y,z range (A): 49.92600 54.79000 53.16300 scale (grids/A): 1.949261 object centre (A): 13.05500 5.404000 14.93850 number of atom coordinates read : 2571 total number of charged atoms : 2428 net assigned charge : 6.000012 assigned positive charge : 387.8779 centred at (gu) : 92.50327 88.40580 90.28380 assigned negative charge : -381.8787 centred at (gu) : 92.29395 88.08142 90.25095 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 77629 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22000 grid for indexing accessible points = 1.400000 m= 26852 mr = 53527 m= 4248 mr = 19622 m= 282 mr = 2657 m= 1 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1224 time to turn everything in is 0.3900000 number of dielectric boundary points 33085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 19156 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) : 0.6497536 object centre at (A) : 13.05500 5.404000 14.93850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9794250E-03 -1.4302486E-03 midg,1,midg; midg,igrid,midg 2.7450781E-02 4.0642433E-02 1,midg,midg; igrid,midg,midg -1.4432202E-02 1.5102244E-02 gauss-seidel spectral radius is 0.9986868 estimated iterations to convergence 219 setup time was (sec) 0.6100000 now iterating at: 21:26:15 rms-change max change #iterations 4.360802 164.7098 at 10iterations 2.065130 75.22847 at 20iterations 0.9822558 30.74915 at 30iterations 0.4672810 15.79059 at 40iterations 0.2213188 6.739976 at 50iterations 0.1050398 3.152224 at 60iterations 4.9752779E-02 1.639259 at 70iterations 2.3781408E-02 0.7422714 at 80iterations 1.1237626E-02 0.3644924 at 90iterations 5.3510605E-03 0.1841393 at 100iterations 2.5375537E-03 7.7377319E-02 at 110iterations 1.2093303E-03 3.6508560E-02 at 120iterations finished qdiffx linear iterations at : 21:26:22 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 1.2093303E-03 3.6508560E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 21:26:22 7.993u 0.197s 0:08.50 96.2% 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 Sun Oct 9 2011 at 21:26:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2571 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.923891 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): -11.90800 38.01800 ymin,ymax (A): -21.99100 32.79900 zmin,zma (A): -11.64300 41.52000 x,y,z range (A): 49.92600 54.79000 53.16300 scale (grids/A): 2.923891 object centre (A): 13.05500 5.404000 14.93850 number of atom coordinates read : 2571 total number of charged atoms : 2428 net assigned charge : 6.000012 assigned positive charge : 387.8779 centred at (gu) : 93.75468 87.60863 90.42557 assigned negative charge : -381.8787 centred at (gu) : 93.44093 87.12205 90.37629 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 179511 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22000 grid for indexing accessible points = 1.400000 m= 87809 mr = 129749 m= 30920 mr = 71661 m= 7786 mr = 24626 m= 1321 mr = 5860 m= 99 mr = 941 m= 5 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.5500001 no. cavity mid-points inaccessible to solvent = 4151 time to turn everything in is 0.9900000 number of dielectric boundary points 74542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 19424 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) : 1.949261 object centre at (A) : 13.05500 5.404000 14.93850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1766666 -0.2178632 midg,1,midg; midg,igrid,midg 0.2350384 0.4101660 1,midg,midg; igrid,midg,midg -0.2584367 0.2332823 gauss-seidel spectral radius is 0.9992734 estimated iterations to convergence 293 setup time was (sec) 1.240000 now iterating at: 21:26:24 rms-change max change #iterations 10.09571 451.3528 at 10iterations 5.882154 114.7615 at 20iterations 3.420754 79.68562 at 30iterations 1.978690 41.41233 at 40iterations 1.143945 21.07130 at 50iterations 0.6618052 12.04901 at 60iterations 0.3815510 6.946720 at 70iterations 0.2200909 3.936304 at 80iterations 0.1272614 2.312057 at 90iterations 7.3393829E-02 1.542742 at 100iterations 4.2365890E-02 0.8464966 at 110iterations 2.4442196E-02 0.4221377 at 120iterations 1.4099614E-02 0.2421150 at 130iterations 8.1370529E-03 0.1405125 at 140iterations 4.6983440E-03 8.2892418E-02 at 150iterations 2.7035272E-03 4.6399117E-02 at 160iterations 1.5607959E-03 2.6203156E-02 at 170iterations 9.0240687E-04 1.6902924E-02 at 180iterations finished qdiffx linear iterations at : 21:26:35 total time elapsed so far: 12.83000 # loops : 180 mean,max change (kT/e) : 9.0240687E-04 1.6902924E-02 energy calculations done at 12.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 21:26:36 12.972u 0.206s 0:13.44 97.9% 0+0k 0+0io 0pf+0w