Sat Oct 8 11:38:02 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 11:38:02 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 = 4198 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5269624 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): -3.087000 64.47000 ymin,ymax (A): -12.09100 38.47800 zmin,zma (A): -19.53400 45.17100 x,y,z range (A): 67.55700 50.56900 64.70500 scale (grids/A): 0.5269624 object centre (A): 30.69150 13.19350 12.81850 number of atom coordinates read : 4198 total number of charged atoms : 4046 net assigned charge : -4.499950 assigned positive charge : 627.0599 centred at (gu) : 88.60853 90.13062 90.68542 assigned negative charge : -631.5626 centred at (gu) : 88.62350 90.23617 90.68245 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7331 nv = 96 ne = 84 npr = 88486 no. pairs analyzed = 88486 no. exposed pairs = 4835 no. arc points = 32400 no. surface atoms = 1651 nbur = 2547 mkacc time = 0.1500000 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 = 1.596000 m= 265 mr = 4105 m= 0 mr = 19 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3310 ## 445 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 9876 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2056509E-10 -1.3772058E-10 midg,1,midg; midg,igrid,midg 3.2819492E-10 -6.3287786E-10 1,midg,midg; igrid,midg,midg -8.6539269E-11 -1.3920595E-10 gauss-seidel spectral radius is 0.9815281 estimated iterations to convergence 61 setup time was (sec) 0.5000000 now iterating at: 11:38:03 rms-change max change #iterations 7.2991438E-02 11.56292 at 10iterations 4.9679577E-03 0.7160034 at 20iterations 6.9435284E-04 8.9234352E-02 at 30iterations 2.0419474E-04 2.1714449E-02 at 40iterations 6.6366243E-05 7.5263977E-03 at 50iterations finished qdiffx linear iterations at : 11:38:06 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 6.6366243E-05 7.5263977E-03 energy calculations done at 3.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 11:38:07 3.934u 0.239s 0:04.54 91.6% 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 Sat Oct 8 2011 at 11:38:07 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 = 4198 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.580887 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): -3.087000 64.47000 ymin,ymax (A): -12.09100 38.47800 zmin,zma (A): -19.53400 45.17100 x,y,z range (A): 67.55700 50.56900 64.70500 scale (grids/A): 1.580887 object centre (A): 30.69150 13.19350 12.81850 number of atom coordinates read : 4198 total number of charged atoms : 4046 net assigned charge : -4.499950 assigned positive charge : 627.0599 centred at (gu) : 85.82465 90.39095 92.05515 assigned negative charge : -631.5626 centred at (gu) : 85.87007 90.70805 92.04682 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 83605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32400 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 25708 mr = 60215 m= 2508 mr = 18102 m= 52 mr = 1199 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 457 time to turn everything in is 0.4300000 number of dielectric boundary points 32357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 365 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 30742 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) : 0.5269624 object centre at (A) : 30.69150 13.19350 12.81850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.9181126E-03 -8.9333272E-03 midg,1,midg; midg,igrid,midg 3.2549792E-03 -1.4074518E-02 1,midg,midg; igrid,midg,midg 1.4063677E-02 1.3301047E-02 gauss-seidel spectral radius is 0.9981713 estimated iterations to convergence 186 setup time was (sec) 0.6900000 now iterating at: 11:38:08 rms-change max change #iterations 3.758969 153.3105 at 10iterations 1.564627 50.41968 at 20iterations 0.6521984 22.51518 at 30iterations 0.2720076 8.330292 at 40iterations 0.1135611 3.482967 at 50iterations 4.7428302E-02 1.583820 at 60iterations 1.9841505E-02 0.6033859 at 70iterations 8.4021818E-03 0.2961044 at 80iterations 3.6138035E-03 0.1186924 at 90iterations 1.6231692E-03 4.9216509E-02 at 100iterations 7.9048460E-04 2.3252487E-02 at 110iterations 4.2458338E-04 1.2713432E-02 at 120iterations finished qdiffx linear iterations at : 11:38:16 total time elapsed so far: 8.810000 # loops : 120 mean,max change (kT/e) : 4.2458338E-04 1.2713432E-02 energy calculations done at 8.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.940000 DelPhi exited at 11:38:16 8.946u 0.265s 0:09.50 96.8% 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 11:38:16 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 = 4198 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.371331 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): -3.087000 64.47000 ymin,ymax (A): -12.09100 38.47800 zmin,zma (A): -19.53400 45.17100 x,y,z range (A): 67.55700 50.56900 64.70500 scale (grids/A): 2.371331 object centre (A): 30.69150 13.19350 12.81850 number of atom coordinates read : 4198 total number of charged atoms : 4046 net assigned charge : -4.499950 assigned positive charge : 627.0599 centred at (gu) : 83.73647 90.58612 93.08257 assigned negative charge : -631.5626 centred at (gu) : 83.80493 91.06201 93.07019 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 194937 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32400 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 91687 mr = 147106 m= 24822 mr = 74141 m= 3781 mr = 18606 m= 174 mr = 2414 m= 5 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 1660 time to turn everything in is 1.040000 number of dielectric boundary points 73097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 32317 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) : 1.580887 object centre at (A) : 30.69150 13.19350 12.81850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2354040 -0.1994240 midg,1,midg; midg,igrid,midg 4.5610834E-02 -0.2123141 1,midg,midg; igrid,midg,midg 0.3795740 0.2918120 gauss-seidel spectral radius is 0.9991569 estimated iterations to convergence 272 setup time was (sec) 1.340000 now iterating at: 11:38:18 rms-change max change #iterations 9.936509 244.7950 at 10iterations 5.650740 137.8473 at 20iterations 3.191588 65.07771 at 30iterations 1.791668 36.23577 at 40iterations 1.000697 21.03191 at 50iterations 0.5600188 10.26083 at 60iterations 0.3120057 5.702682 at 70iterations 0.1735180 3.317555 at 80iterations 9.6636645E-02 1.783686 at 90iterations 5.3594008E-02 1.077370 at 100iterations 2.9807227E-02 0.5487385 at 110iterations 1.6548751E-02 0.3044100 at 120iterations 9.2191054E-03 0.1729202 at 130iterations 5.1519182E-03 8.9494944E-02 at 140iterations 2.8915554E-03 6.0331345E-02 at 150iterations 1.6411466E-03 2.8991699E-02 at 160iterations 9.5104205E-04 1.7452240E-02 at 170iterations 5.6901097E-04 1.0864258E-02 at 180iterations finished qdiffx linear iterations at : 11:38:31 total time elapsed so far: 14.54000 # loops : 180 mean,max change (kT/e) : 5.6901097E-04 1.0864258E-02 energy calculations done at 14.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.67000 DelPhi exited at 11:38:32 14.674u 0.280s 0:15.25 98.0% 0+0k 0+0io 0pf+0w