Mon Oct 10 19:32:57 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 19:32:57 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: SER 360 has a net charge of 0.5000 !!! WARNING: CME 1 has a net charge of 0.1000 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: 0.5569462 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): -34.84400 21.56500 ymin,ymax (A): -16.48600 30.44400 zmin,zma (A): 10.62900 74.54900 x,y,z range (A): 56.40900 46.93000 63.92001 scale (grids/A): 0.5569462 object centre (A): -6.639501 6.979000 42.58900 number of atom coordinates read : 2999 total number of charged atoms : 2856 net assigned charge : 8.100025 assigned positive charge : 444.9132 centred at (gu) : 89.97729 90.98745 90.78918 assigned negative charge : -436.8145 centred at (gu) : 89.94273 90.85567 90.87915 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6029 nv = 96 ne = 84 npr = 60585 no. pairs analyzed = 60585 no. exposed pairs = 3703 no. arc points = 26398 no. surface atoms = 1250 nbur = 1749 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 = 1.540000 m= 232 mr = 3169 m= 0 mr = 8 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.3400000 number of dielectric boundary points 3084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2614 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7798 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3480390E-09 -1.6064054E-10 midg,1,midg; midg,igrid,midg -4.1941353E-10 2.5793903E-09 1,midg,midg; igrid,midg,midg 4.2607304E-10 1.0919637E-09 gauss-seidel spectral radius is 0.9833725 estimated iterations to convergence 64 setup time was (sec) 0.5800000 now iterating at: 19:32:58 rms-change max change #iterations 8.0557980E-02 13.30930 at 10iterations 5.6362464E-03 0.9232779 at 20iterations 4.0639483E-04 6.3473225E-02 at 30iterations 3.3190448E-05 5.6610107E-03 at 40iterations 5.2498326E-06 1.5010834E-03 at 50iterations finished qdiffx linear iterations at : 19:33:02 total time elapsed so far: 4.690000 # loops : 50 mean,max change (kT/e) : 5.2498326E-06 1.5010834E-03 energy calculations done at 4.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.860000 DelPhi exited at 19:33:02 4.860u 0.398s 0:05.59 93.9% 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 19:33:02 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: SER 360 has a net charge of 0.5000 !!! WARNING: CME 1 has a net charge of 0.1000 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: 1.670838 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): -34.84400 21.56500 ymin,ymax (A): -16.48600 30.44400 zmin,zma (A): 10.62900 74.54900 x,y,z range (A): 56.40900 46.93000 63.92001 scale (grids/A): 1.670838 object centre (A): -6.639501 6.979000 42.58900 number of atom coordinates read : 2999 total number of charged atoms : 2856 net assigned charge : 8.100025 assigned positive charge : 444.9132 centred at (gu) : 89.93069 92.96161 92.36675 assigned negative charge : -436.8145 centred at (gu) : 89.82809 92.56678 92.63741 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 67044 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26398 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19985 mr = 45785 m= 2084 mr = 13824 m= 57 mr = 1161 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3157 time to turn everything in is 0.5400000 number of dielectric boundary points 28396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 333 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 22024 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) : 0.5569462 object centre at (A) : -6.639501 6.979000 42.58900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4389746E-03 -2.1030942E-03 midg,1,midg; midg,igrid,midg -4.2392202E-03 1.2774783E-02 1,midg,midg; igrid,midg,midg 1.3400510E-02 1.7207986E-02 gauss-seidel spectral radius is 0.9982659 estimated iterations to convergence 191 setup time was (sec) 0.8400000 now iterating at: 19:33:03 rms-change max change #iterations 3.460251 156.8307 at 10iterations 1.460386 51.87865 at 20iterations 0.6203082 22.57656 at 30iterations 0.2640513 9.426058 at 40iterations 0.1126532 4.224457 at 50iterations 4.7839478E-02 1.847740 at 60iterations 2.0303980E-02 0.7021885 at 70iterations 8.6509837E-03 0.3497463 at 80iterations 3.6742617E-03 0.1305580 at 90iterations 1.5678187E-03 6.0577393E-02 at 100iterations 6.6585740E-04 2.4932861E-02 at 110iterations 2.8472368E-04 9.7398758E-03 at 120iterations finished qdiffx linear iterations at : 19:33:14 total time elapsed so far: 11.24000 # loops : 120 mean,max change (kT/e) : 2.8472368E-04 9.7398758E-03 energy calculations done at 11.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.42000 DelPhi exited at 19:33:15 11.420u 0.434s 0:12.31 96.2% 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 Mon Oct 10 2011 at 19:33:15 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: SER 360 has a net charge of 0.5000 !!! WARNING: CME 1 has a net charge of 0.1000 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: 2.506258 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): -34.84400 21.56500 ymin,ymax (A): -16.48600 30.44400 zmin,zma (A): 10.62900 74.54900 x,y,z range (A): 56.40900 46.93000 63.92001 scale (grids/A): 2.506258 object centre (A): -6.639501 6.979000 42.58900 number of atom coordinates read : 2999 total number of charged atoms : 2856 net assigned charge : 8.100025 assigned positive charge : 444.9132 centred at (gu) : 89.89585 94.44199 93.54998 assigned negative charge : -436.8145 centred at (gu) : 89.74212 93.84989 93.95604 start vw surface at 0.1200000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 155972 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26398 grid for indexing accessible points = 1.400000 m= 69983 mr = 112033 m= 19378 mr = 55665 m= 3315 mr = 14691 m= 251 mr = 2358 m= 3 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 10433 time to turn everything in is 1.300000 number of dielectric boundary points 64036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 22818 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) : 1.670838 object centre at (A) : -6.639501 6.979000 42.58900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2198050 6.9987699E-02 midg,1,midg; midg,igrid,midg -6.5720655E-02 0.1398948 1,midg,midg; igrid,midg,midg 0.1664355 0.2986518 gauss-seidel spectral radius is 0.9991641 estimated iterations to convergence 273 setup time was (sec) 1.630000 now iterating at: 19:33:17 rms-change max change #iterations 8.734222 294.8857 at 10iterations 4.893753 114.6822 at 20iterations 2.723205 57.06229 at 30iterations 1.521458 35.10435 at 40iterations 0.8427313 24.74619 at 50iterations 0.4687427 10.98707 at 60iterations 0.2602630 5.493984 at 70iterations 0.1444007 2.965302 at 80iterations 8.0084838E-02 1.535324 at 90iterations 4.4403110E-02 0.9019837 at 100iterations 2.4650525E-02 0.4989567 at 110iterations 1.3666269E-02 0.2955589 at 120iterations 7.5758211E-03 0.1636009 at 130iterations 4.2015519E-03 8.5135460E-02 at 140iterations 2.3302766E-03 4.9572051E-02 at 150iterations 1.2915464E-03 2.6527405E-02 at 160iterations 7.1848260E-04 1.6021490E-02 at 170iterations 4.0074697E-04 9.1371536E-03 at 180iterations finished qdiffx linear iterations at : 19:33:34 total time elapsed so far: 18.51000 # loops : 180 mean,max change (kT/e) : 4.0074697E-04 9.1371536E-03 energy calculations done at 18.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.68000 DelPhi exited at 19:33:34 18.682u 0.463s 0:19.84 96.4% 0+0k 0+0io 0pf+0w