Thu Jan 19 14:00:47 PST 2012 #!/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+sph2.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 = amb2.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 Thu Jan 19 2012 at 14:00:51 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6721 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: HEM 1106 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4330847 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): -5.189000 77.01200 ymin,ymax (A): -0.6610000 75.88600 zmin,zma (A): 167.5770 235.2910 x,y,z range (A): 82.20100 76.54700 67.71400 scale (grids/A): 0.4330847 object centre (A): 35.91150 37.61250 201.4340 number of atom coordinates read : 6721 total number of charged atoms : 6551 net assigned charge : -5.659947 assigned positive charge : 1018.406 centred at (gu) : 88.79877 90.11893 89.40212 assigned negative charge : -1024.075 centred at (gu) : 88.80712 90.18919 89.37442 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7425 nv = 96 ne = 84 npr = 136618 no. pairs analyzed = 136618 no. exposed pairs = 8665 no. arc points = 58560 no. surface atoms = 2926 nbur = 3795 mkacc time = 0.2400000 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 = 1.932000 m= 178 mr = 3527 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 4074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4904 ## 1007 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 10290 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1404770E-12 5.7015802E-13 midg,1,midg; midg,igrid,midg 3.6877675E-12 -6.9241882E-12 1,midg,midg; igrid,midg,midg -1.0531446E-12 -1.3861415E-12 gauss-seidel spectral radius is 0.9729378 estimated iterations to convergence 51 setup time was (sec) 0.6100000 now iterating at: 14:00:55 rms-change max change #iterations 3.2485485E-02 5.225116 at 10iterations 1.7024705E-03 0.2861118 at 20iterations 4.9492077E-04 8.8591576E-02 at 30iterations 1.8135118E-04 3.2324791E-02 at 40iterations 6.6406734E-05 1.1793137E-02 at 50iterations finished qdiffx linear iterations at : 14:01:06 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 6.6406734E-05 1.1793137E-02 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 14:01:07 4.135u 0.189s 0:16.20 26.6% 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 Thu Jan 19 2012 at 14:01:09 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6721 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: HEM 1106 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.299254 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): -5.189000 77.01200 ymin,ymax (A): -0.6610000 75.88600 zmin,zma (A): 167.5770 235.2910 x,y,z range (A): 82.20100 76.54700 67.71400 scale (grids/A): 1.299254 object centre (A): 35.91150 37.61250 201.4340 number of atom coordinates read : 6721 total number of charged atoms : 6551 net assigned charge : -5.659947 assigned positive charge : 1018.406 centred at (gu) : 86.39432 90.35494 88.20454 assigned negative charge : -1024.075 centred at (gu) : 86.42135 90.56690 88.12311 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 87203 reading accessible surface arcs data from file ARCDAT no. of arc points read = 58560 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 19978 mr = 57708 m= 1054 mr = 11839 m= 6 mr = 286 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 652 time to turn everything in is 0.4600000 number of dielectric boundary points 38408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1072 ## 31 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 45569 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) : 0.4330847 object centre at (A) : 35.91150 37.61250 201.4340 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8024320E-04 -4.0050744E-04 midg,1,midg; midg,igrid,midg -5.4154039E-04 -7.7300966E-03 1,midg,midg; igrid,midg,midg -2.2149521E-03 1.0538459E-03 gauss-seidel spectral radius is 0.9974396 estimated iterations to convergence 158 setup time was (sec) 0.6900000 now iterating at: 14:01:14 rms-change max change #iterations 3.116935 139.5518 at 10iterations 1.105238 46.30732 at 20iterations 0.3910402 12.90383 at 30iterations 0.1386105 4.969271 at 40iterations 4.9301963E-02 1.690723 at 50iterations 1.7525947E-02 0.6628380 at 60iterations 6.3136169E-03 0.2301335 at 70iterations 2.3664366E-03 8.8133335E-02 at 80iterations 9.8069117E-04 3.5978317E-02 at 90iterations 4.9467525E-04 1.9279957E-02 at 100iterations 3.0026966E-04 1.1886597E-02 at 110iterations 1.9976837E-04 7.3709488E-03 at 120iterations finished qdiffx linear iterations at : 14:01:38 total time elapsed so far: 8.630000 # loops : 120 mean,max change (kT/e) : 1.9976837E-04 7.3709488E-03 energy calculations done at 8.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.770000 DelPhi exited at 14:01:40 8.768u 0.264s 0:30.98 29.1% 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 Thu Jan 19 2012 at 14:01:42 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6721 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: HEM 1106 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.948881 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): -5.189000 77.01200 ymin,ymax (A): -0.6610000 75.88600 zmin,zma (A): 167.5770 235.2910 x,y,z range (A): 82.20100 76.54700 67.71400 scale (grids/A): 1.948881 object centre (A): 35.91150 37.61250 201.4340 number of atom coordinates read : 6721 total number of charged atoms : 6551 net assigned charge : -5.659947 assigned positive charge : 1018.406 centred at (gu) : 84.59097 90.53205 87.30609 assigned negative charge : -1024.075 centred at (gu) : 84.63187 90.85045 87.18459 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 204536 reading accessible surface arcs data from file ARCDAT no. of arc points read = 58560 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 78439 mr = 144141 m= 14009 mr = 57757 m= 1056 mr = 8921 m= 12 mr = 423 m= 0 mr = 0 time to grow re-entrant surface = 0.5799999 no. cavity mid-points inaccessible to solvent = 2186 time to turn everything in is 1.070000 number of dielectric boundary points 86810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 313 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 51694 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) : 1.299254 object centre at (A) : 35.91150 37.61250 201.4340 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0402251E-02 -1.4320397E-02 midg,1,midg; midg,igrid,midg -2.8717918E-02 -0.1503267 1,midg,midg; igrid,midg,midg -4.0613323E-02 0.1206863 gauss-seidel spectral radius is 0.9989876 estimated iterations to convergence 249 setup time was (sec) 1.330000 now iterating at: 14:01:49 rms-change max change #iterations 9.504496 326.8125 at 10iterations 5.155705 121.4617 at 20iterations 2.766634 75.91989 at 30iterations 1.478245 36.85308 at 40iterations 0.7866858 17.25649 at 50iterations 0.4169991 10.47806 at 60iterations 0.2204768 4.791632 at 70iterations 0.1162265 2.881226 at 80iterations 6.1179120E-02 1.304359 at 90iterations 3.2220688E-02 0.7695923 at 100iterations 1.6938321E-02 0.3581905 at 110iterations 8.9173978E-03 0.1833429 at 120iterations 4.6846028E-03 0.1174994 at 130iterations 2.4654060E-03 5.6550980E-02 at 140iterations 1.3060403E-03 2.9334068E-02 at 150iterations 6.9999963E-04 1.5275002E-02 at 160iterations 3.8360964E-04 8.8310242E-03 at 170iterations 2.1830760E-04 5.5103302E-03 at 180iterations finished qdiffx linear iterations at : 14:02:27 total time elapsed so far: 14.17000 # loops : 180 mean,max change (kT/e) : 2.1830760E-04 5.5103302E-03 energy calculations done at 14.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.31000 DelPhi exited at 14:02:29 14.315u 0.221s 0:47.70 30.4% 0+0k 0+0io 0pf+0w