Sun Oct 9 15:40:54 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 15:40:55 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 = 5659 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: 0.5053230 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): 67.29600 137.7460 ymin,ymax (A): -6.234000 56.98200 zmin,zma (A): -3.312000 65.75400 x,y,z range (A): 70.44999 63.21600 69.06599 scale (grids/A): 0.5053230 object centre (A): 102.5210 25.37400 31.22100 number of atom coordinates read : 5659 total number of charged atoms : 5488 net assigned charge : -3.499964 assigned positive charge : 865.5180 centred at (gu) : 89.94059 90.84220 90.24033 assigned negative charge : -869.0259 centred at (gu) : 90.00172 90.76876 90.33935 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8814 nv = 96 ne = 84 npr = 117164 no. pairs analyzed = 117164 no. exposed pairs = 6427 no. arc points = 44364 no. surface atoms = 2156 nbur = 3503 mkacc time = 0.2000000 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 = 1.708000 m= 292 mr = 4830 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.3800000 number of dielectric boundary points 4262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4294 ## 629 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 12030 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9244466E-10 -3.1194830E-10 midg,1,midg; midg,igrid,midg -1.8096773E-10 1.7975556E-10 1,midg,midg; igrid,midg,midg 1.1407325E-10 -1.9199062E-10 gauss-seidel spectral radius is 0.9800228 estimated iterations to convergence 58 setup time was (sec) 0.5500000 now iterating at: 15:40:55 rms-change max change #iterations 7.0942014E-02 9.472885 at 10iterations 4.7278912E-03 0.6914825 at 20iterations 7.5079314E-04 0.1192894 at 30iterations 2.0188662E-04 2.9689789E-02 at 40iterations 5.8675181E-05 7.7972412E-03 at 50iterations finished qdiffx linear iterations at : 15:40:58 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 5.8675181E-05 7.7972412E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 15:40:59 3.605u 0.216s 0:04.13 92.2% 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 15:40:59 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 = 5659 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.515969 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): 67.29600 137.7460 ymin,ymax (A): -6.234000 56.98200 zmin,zma (A): -3.312000 65.75400 x,y,z range (A): 70.44999 63.21600 69.06599 scale (grids/A): 1.515969 object centre (A): 102.5210 25.37400 31.22100 number of atom coordinates read : 5659 total number of charged atoms : 5488 net assigned charge : -3.499964 assigned positive charge : 865.5180 centred at (gu) : 89.81994 92.52521 90.71904 assigned negative charge : -869.0259 centred at (gu) : 90.00476 92.30607 91.01797 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 100937 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44364 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 29196 mr = 71593 m= 2461 mr = 20037 m= 40 mr = 1115 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3435 time to turn everything in is 0.4900000 number of dielectric boundary points 39889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 581 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 41063 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) : 0.5053230 object centre at (A) : 102.5210 25.37400 31.22100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1716493E-03 1.1834761E-03 midg,1,midg; midg,igrid,midg -1.2037206E-02 6.2133381E-03 1,midg,midg; igrid,midg,midg -1.7223123E-02 -1.0130566E-02 gauss-seidel spectral radius is 0.9981312 estimated iterations to convergence 184 setup time was (sec) 0.7100000 now iterating at: 15:41:00 rms-change max change #iterations 4.153806 164.3625 at 10iterations 1.711190 52.22079 at 20iterations 0.7034301 20.88136 at 30iterations 0.2906255 8.837219 at 40iterations 0.1201186 3.899049 at 50iterations 4.9686257E-02 1.375654 at 60iterations 2.0574182E-02 0.6268578 at 70iterations 8.5368352E-03 0.2515726 at 80iterations 3.5632702E-03 0.1142740 at 90iterations 1.5168859E-03 4.3640137E-02 at 100iterations 6.6086388E-04 2.1865845E-02 at 110iterations 3.0409015E-04 9.2506409E-03 at 120iterations finished qdiffx linear iterations at : 15:41:07 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 3.0409015E-04 9.2506409E-03 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 15:41:07 8.016u 0.237s 0:08.61 95.7% 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 15:41:07 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 = 5659 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.273953 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): 67.29600 137.7460 ymin,ymax (A): -6.234000 56.98200 zmin,zma (A): -3.312000 65.75400 x,y,z range (A): 70.44999 63.21600 69.06599 scale (grids/A): 2.273953 object centre (A): 102.5210 25.37400 31.22100 number of atom coordinates read : 5659 total number of charged atoms : 5488 net assigned charge : -3.499964 assigned positive charge : 865.5180 centred at (gu) : 89.72948 93.78728 91.07830 assigned negative charge : -869.0259 centred at (gu) : 90.00713 93.45927 91.52676 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 235882 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44364 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 105335 mr = 175985 m= 26754 mr = 83598 m= 3600 mr = 19895 m= 168 mr = 2237 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 11608 time to turn everything in is 1.190000 number of dielectric boundary points 89983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 43765 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) : 1.515969 object centre at (A) : 102.5210 25.37400 31.22100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1620737E-02 0.1432841 midg,1,midg; midg,igrid,midg -0.2592098 0.2194764 1,midg,midg; igrid,midg,midg -0.5162711 0.1130635 gauss-seidel spectral radius is 0.9991778 estimated iterations to convergence 275 setup time was (sec) 1.430000 now iterating at: 15:41:09 rms-change max change #iterations 11.13165 328.9928 at 10iterations 6.385424 138.8534 at 20iterations 3.629791 82.73273 at 30iterations 2.055914 44.51210 at 40iterations 1.160859 31.25156 at 50iterations 0.6545444 13.17697 at 60iterations 0.3675297 7.313568 at 70iterations 0.2065495 3.446980 at 80iterations 0.1156040 2.190074 at 90iterations 6.4806521E-02 1.288643 at 100iterations 3.6243565E-02 0.6585426 at 110iterations 2.0268701E-02 0.3943768 at 120iterations 1.1344621E-02 0.1927481 at 130iterations 6.3348259E-03 0.1067047 at 140iterations 3.5508261E-03 5.9644699E-02 at 150iterations 1.9878412E-03 3.3287048E-02 at 160iterations 1.1166292E-03 2.0339489E-02 at 170iterations 6.2690623E-04 1.1308670E-02 at 180iterations finished qdiffx linear iterations at : 15:41:21 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 6.2690623E-04 1.1308670E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 15:41:21 13.233u 0.224s 0:13.73 97.9% 0+0k 0+0io 0pf+0w