Mon Oct 10 23:14:33 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 Mon Oct 10 2011 at 23:14:33 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 = 2562 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5790595 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): -11.03700 50.44200 ymin,ymax (A): -7.126000 43.22400 zmin,zma (A): -7.543000 33.15700 x,y,z range (A): 61.47900 50.35000 40.70000 scale (grids/A): 0.5790595 object centre (A): 19.70250 18.04900 12.80700 number of atom coordinates read : 2562 total number of charged atoms : 2426 net assigned charge : 8.500022 assigned positive charge : 384.3568 centred at (gu) : 92.81853 90.41689 90.15771 assigned negative charge : -375.8575 centred at (gu) : 92.69231 90.34149 90.23473 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5364 nv = 96 ne = 84 npr = 53272 no. pairs analyzed = 53272 no. exposed pairs = 2981 no. arc points = 21168 no. surface atoms = 997 nbur = 1565 mkacc time = 0.1400000 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 = 1.484000 m= 228 mr = 2908 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.2800000 number of dielectric boundary points 2674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2048 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6960 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9618448E-09 3.2647804E-10 midg,1,midg; midg,igrid,midg 3.2222824E-10 3.3533805E-09 1,midg,midg; igrid,midg,midg -2.7058983E-10 7.6759497E-09 gauss-seidel spectral radius is 0.9845634 estimated iterations to convergence 66 setup time was (sec) 0.5600000 now iterating at: 23:14:34 rms-change max change #iterations 9.2064947E-02 16.68446 at 10iterations 7.8936089E-03 1.592331 at 20iterations 1.0811416E-03 0.2789307 at 30iterations 2.5766710E-04 7.1453094E-02 at 40iterations 6.6512264E-05 1.9012451E-02 at 50iterations finished qdiffx linear iterations at : 23:14:38 total time elapsed so far: 4.820000 # loops : 50 mean,max change (kT/e) : 6.6512264E-05 1.9012451E-02 energy calculations done at 4.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.000000 DelPhi exited at 23:14:39 5.004u 0.452s 0:06.01 90.6% 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 Mon Oct 10 2011 at 23:14:39 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 = 2562 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.737179 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): -11.03700 50.44200 ymin,ymax (A): -7.126000 43.22400 zmin,zma (A): -7.543000 33.15700 x,y,z range (A): 61.47900 50.35000 40.70000 scale (grids/A): 1.737179 object centre (A): 19.70250 18.04900 12.80700 number of atom coordinates read : 2562 total number of charged atoms : 2426 net assigned charge : 8.500022 assigned positive charge : 384.3568 centred at (gu) : 98.45524 91.25019 90.47260 assigned negative charge : -375.8575 centred at (gu) : 98.07655 91.02440 90.70394 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59513 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21168 grid for indexing accessible points = 1.400000 m= 18004 mr = 41097 m= 1970 mr = 12649 m= 57 mr = 1051 m= 0 mr = 5 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1861 time to turn everything in is 0.4900000 number of dielectric boundary points 24742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18855 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) : 0.5790595 object centre at (A) : 19.70250 18.04900 12.80700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4875147E-02 6.5581794E-03 midg,1,midg; midg,igrid,midg 1.1466715E-02 1.9938199E-02 1,midg,midg; igrid,midg,midg 2.3925947E-03 -2.7325624E-03 gauss-seidel spectral radius is 0.9983441 estimated iterations to convergence 195 setup time was (sec) 0.8700000 now iterating at: 23:14:40 rms-change max change #iterations 3.425949 186.8515 at 10iterations 1.481205 65.85212 at 20iterations 0.6432604 24.86892 at 30iterations 0.2790774 10.47414 at 40iterations 0.1216617 4.667065 at 50iterations 5.2831236E-02 2.163734 at 60iterations 2.3073653E-02 0.8035202 at 70iterations 1.0128965E-02 0.3820572 at 80iterations 4.5471247E-03 0.1657740 at 90iterations 2.0873442E-03 8.4007263E-02 at 100iterations 1.0105784E-03 4.0287018E-02 at 110iterations 5.1296799E-04 2.5039673E-02 at 120iterations finished qdiffx linear iterations at : 23:14:51 total time elapsed so far: 11.80000 # loops : 120 mean,max change (kT/e) : 5.1296799E-04 2.5039673E-02 energy calculations done at 11.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 23:14:52 11.973u 0.495s 0:13.04 95.5% 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 Mon Oct 10 2011 at 23:14:52 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 = 2562 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.605768 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): -11.03700 50.44200 ymin,ymax (A): -7.126000 43.22400 zmin,zma (A): -7.543000 33.15700 x,y,z range (A): 61.47900 50.35000 40.70000 scale (grids/A): 2.605768 object centre (A): 19.70250 18.04900 12.80700 number of atom coordinates read : 2562 total number of charged atoms : 2426 net assigned charge : 8.500022 assigned positive charge : 384.3568 centred at (gu) : 102.6826 91.87523 90.70876 assigned negative charge : -375.8575 centred at (gu) : 102.1148 91.53636 91.05589 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 138064 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21168 grid for indexing accessible points = 1.400000 m= 62289 mr = 100144 m= 18290 mr = 49894 m= 3310 mr = 14043 m= 265 mr = 2320 m= 5 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 6634 time to turn everything in is 1.220000 number of dielectric boundary points 55697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 19398 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) : 1.737179 object centre at (A) : 19.70250 18.04900 12.80700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1679535 7.9112656E-02 midg,1,midg; midg,igrid,midg 0.1701614 0.2201048 1,midg,midg; igrid,midg,midg 5.3273201E-02 -8.7588966E-02 gauss-seidel spectral radius is 0.9991707 estimated iterations to convergence 274 setup time was (sec) 1.620000 now iterating at: 23:14:54 rms-change max change #iterations 8.465276 273.2671 at 10iterations 4.755946 112.4156 at 20iterations 2.657833 69.39245 at 30iterations 1.491040 32.80574 at 40iterations 0.8302923 18.59332 at 50iterations 0.4628973 10.01206 at 60iterations 0.2572897 5.494853 at 70iterations 0.1435098 3.080345 at 80iterations 7.9708122E-02 1.780914 at 90iterations 4.4526782E-02 0.9066010 at 100iterations 2.4788706E-02 0.5261002 at 110iterations 1.3850821E-02 0.2825546 at 120iterations 7.7848244E-03 0.1737976 at 130iterations 4.4085681E-03 0.1012154 at 140iterations 2.5396440E-03 5.9608459E-02 at 150iterations 1.5051212E-03 3.8707733E-02 at 160iterations 9.2795183E-04 2.4902344E-02 at 170iterations 5.9754413E-04 1.6841888E-02 at 180iterations finished qdiffx linear iterations at : 23:15:11 total time elapsed so far: 19.04000 # loops : 180 mean,max change (kT/e) : 5.9754413E-04 1.6841888E-02 energy calculations done at 19.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.20000 DelPhi exited at 23:15:12 19.209u 0.518s 0:20.07 98.2% 0+0k 0+0io 0pf+0w