Sat Oct 15 14:18:10 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 Sat Oct 15 2011 at 14:18:10 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4812 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5103943 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): -18.54000 37.18900 ymin,ymax (A): -30.72100 34.14100 zmin,zma (A): -4.083000 65.66700 x,y,z range (A): 55.72900 64.86200 69.75000 scale (grids/A): 0.5103943 object centre (A): 9.324502 1.710001 30.79200 number of atom coordinates read : 4812 total number of charged atoms : 4565 net assigned charge : 6.800033 assigned positive charge : 721.9744 centred at (gu) : 90.19844 90.52422 88.46063 assigned negative charge : -715.1788 centred at (gu) : 90.08488 90.59927 88.44144 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8007 nv = 96 ne = 84 npr = 96617 no. pairs analyzed = 96617 no. exposed pairs = 6080 no. arc points = 42849 no. surface atoms = 2037 nbur = 2775 mkacc time = 0.1600000 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 = 1.680000 m= 275 mr = 4116 m= 0 mr = 3 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4163 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4123 ## 596 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 10597 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9366936E-11 9.8222236E-11 midg,1,midg; midg,igrid,midg 2.5061031E-10 -1.1319014E-10 1,midg,midg; igrid,midg,midg -1.8859744E-10 4.0478149E-10 gauss-seidel spectral radius is 0.9803746 estimated iterations to convergence 59 setup time was (sec) 0.5300000 now iterating at: 14:18:11 rms-change max change #iterations 6.6182099E-02 11.50685 at 10iterations 3.8729906E-03 0.6047564 at 20iterations 3.6086285E-04 4.9377441E-02 at 30iterations 1.0575488E-04 1.5983582E-02 at 40iterations 4.1429765E-05 6.4973831E-03 at 50iterations finished qdiffx linear iterations at : 14:18:14 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 4.1429765E-05 6.4973831E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 14:18:15 4.051u 0.207s 0:04.60 92.3% 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 15 2011 at 14:18:15 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4812 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.531183 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): -18.54000 37.18900 ymin,ymax (A): -30.72100 34.14100 zmin,zma (A): -4.083000 65.66700 x,y,z range (A): 55.72900 64.86200 69.75000 scale (grids/A): 1.531183 object centre (A): 9.324502 1.710001 30.79200 number of atom coordinates read : 4812 total number of charged atoms : 4565 net assigned charge : 6.800033 assigned positive charge : 721.9744 centred at (gu) : 90.59389 91.57102 85.38056 assigned negative charge : -715.1788 centred at (gu) : 90.25445 91.79745 85.32413 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 90805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42849 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25955 mr = 62297 m= 2188 mr = 16996 m= 49 mr = 873 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 167 time to turn everything in is 0.4400000 number of dielectric boundary points 38829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 578 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 34361 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) : 0.5103943 object centre at (A) : 9.324502 1.710001 30.79200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9124706E-03 2.0568224E-02 midg,1,midg; midg,igrid,midg 1.3059392E-02 -1.4148592E-02 1,midg,midg; igrid,midg,midg -1.7838207E-03 1.1922013E-02 gauss-seidel spectral radius is 0.9981186 estimated iterations to convergence 183 setup time was (sec) 0.6800000 now iterating at: 14:18:15 rms-change max change #iterations 3.775524 167.8947 at 10iterations 1.545748 48.40187 at 20iterations 0.6352932 19.59995 at 30iterations 0.2607664 8.347218 at 40iterations 0.1070392 3.400417 at 50iterations 4.4167411E-02 1.342565 at 60iterations 1.8128097E-02 0.5943985 at 70iterations 7.4699000E-03 0.2387981 at 80iterations 3.0889323E-03 0.1006222 at 90iterations 1.2726450E-03 4.1910172E-02 at 100iterations 5.3104857E-04 1.6850471E-02 at 110iterations 2.2828915E-04 7.7552795E-03 at 120iterations finished qdiffx linear iterations at : 14:18:30 total time elapsed so far: 8.160000 # loops : 120 mean,max change (kT/e) : 2.2828915E-04 7.7552795E-03 energy calculations done at 8.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.280000 DelPhi exited at 14:18:31 8.285u 0.225s 0:16.07 52.8% 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 15 2011 at 14:18:31 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4812 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.296774 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): -18.54000 37.18900 ymin,ymax (A): -30.72100 34.14100 zmin,zma (A): -4.083000 65.66700 x,y,z range (A): 55.72900 64.86200 69.75000 scale (grids/A): 2.296774 object centre (A): 9.324502 1.710001 30.79200 number of atom coordinates read : 4812 total number of charged atoms : 4565 net assigned charge : 6.800033 assigned positive charge : 721.9744 centred at (gu) : 90.89041 92.35606 83.07052 assigned negative charge : -715.1788 centred at (gu) : 90.38151 92.69614 82.98618 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 211632 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42849 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 93699 mr = 153181 m= 23164 mr = 72681 m= 3065 mr = 16339 m= 173 mr = 1763 m= 0 mr = 78 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 557 time to turn everything in is 1.110000 number of dielectric boundary points 87691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 36406 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) : 1.531183 object centre at (A) : 9.324502 1.710001 30.79200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1537237 0.5047915 midg,1,midg; midg,igrid,midg 0.2500397 -0.3049332 1,midg,midg; igrid,midg,midg -1.5729075E-02 0.1741473 gauss-seidel spectral radius is 0.9991662 estimated iterations to convergence 274 setup time was (sec) 1.390000 now iterating at: 14:18:32 rms-change max change #iterations 10.32644 310.8552 at 10iterations 5.917454 142.1581 at 20iterations 3.374759 75.31789 at 30iterations 1.907473 43.88517 at 40iterations 1.076453 21.27406 at 50iterations 0.6065802 13.08677 at 60iterations 0.3408751 7.283562 at 70iterations 0.1906917 3.813870 at 80iterations 0.1066834 2.238979 at 90iterations 5.9605520E-02 1.175542 at 100iterations 3.3246089E-02 0.6976395 at 110iterations 1.8563354E-02 0.3451729 at 120iterations 1.0343782E-02 0.2059059 at 130iterations 5.7654735E-03 0.1223121 at 140iterations 3.2217631E-03 5.9869766E-02 at 150iterations 1.8007134E-03 3.4603119E-02 at 160iterations 1.0138403E-03 1.9965172E-02 at 170iterations 5.7846250E-04 1.1650085E-02 at 180iterations finished qdiffx linear iterations at : 14:18:45 total time elapsed so far: 14.05000 # loops : 180 mean,max change (kT/e) : 5.7846250E-04 1.1650085E-02 energy calculations done at 14.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.18000 DelPhi exited at 14:18:45 14.183u 0.252s 0:14.71 98.0% 0+0k 0+0io 0pf+0w