Mon Oct 10 17:03:40 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+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 Mon Oct 10 2011 at 17:03:40 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 !!! WARNING: ASL 152 has a net charge of -0.1000 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 0.5526577 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): 17.47000 64.88600 ymin,ymax (A): -9.516000 41.58700 zmin,zma (A): -1.976000 62.44000 x,y,z range (A): 47.41600 51.10300 64.41600 scale (grids/A): 0.5526577 object centre (A): 41.17800 16.03550 30.23200 number of atom coordinates read : 2765 total number of charged atoms : 2622 net assigned charge : 5.806027 assigned positive charge : 409.5786 centred at (gu) : 90.49237 89.33238 89.25662 assigned negative charge : -403.7736 centred at (gu) : 90.47778 89.18353 89.28425 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5550 nv = 96 ne = 84 npr = 55621 no. pairs analyzed = 55621 no. exposed pairs = 3711 no. arc points = 25582 no. surface atoms = 1239 nbur = 1526 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 = 1.540000 m= 229 mr = 2764 m= 0 mr = 10 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3005 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2628 ## 310 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7171 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2286228E-10 2.2033599E-10 midg,1,midg; midg,igrid,midg -8.2661572E-10 1.3612412E-09 1,midg,midg; igrid,midg,midg 3.2276462E-10 6.6099543E-10 gauss-seidel spectral radius is 0.9831021 estimated iterations to convergence 63 setup time was (sec) 0.6000000 now iterating at: 17:03:41 rms-change max change #iterations 7.4214391E-02 13.97094 at 10iterations 5.1250113E-03 1.007156 at 20iterations 3.7494567E-04 6.8223953E-02 at 30iterations 3.3757475E-05 5.5038929E-03 at 40iterations 4.0947161E-06 5.5122375E-04 at 50iterations finished qdiffx linear iterations at : 17:03:45 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 4.0947161E-06 5.5122375E-04 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 17:03:46 4.489u 0.404s 0:06.16 79.2% 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 17:03:46 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 !!! WARNING: ASL 152 has a net charge of -0.1000 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 1.657973 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): 17.47000 64.88600 ymin,ymax (A): -9.516000 41.58700 zmin,zma (A): -1.976000 62.44000 x,y,z range (A): 47.41600 51.10300 64.41600 scale (grids/A): 1.657973 object centre (A): 41.17800 16.03550 30.23200 number of atom coordinates read : 2765 total number of charged atoms : 2622 net assigned charge : 5.806027 assigned positive charge : 409.5786 centred at (gu) : 91.47629 87.99667 87.76935 assigned negative charge : -403.7736 centred at (gu) : 91.43327 87.55051 87.85262 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 61179 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25582 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18678 mr = 40664 m= 2050 mr = 12433 m= 52 mr = 977 m= 0 mr = 6 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 82 time to turn everything in is 0.5100000 number of dielectric boundary points 27879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 273 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 20133 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) : 0.5526577 object centre at (A) : 41.17800 16.03550 30.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3218123E-02 1.7380895E-02 midg,1,midg; midg,igrid,midg -7.4287700E-03 9.4232755E-03 1,midg,midg; igrid,midg,midg 7.4861350E-04 1.4352615E-03 gauss-seidel spectral radius is 0.9982214 estimated iterations to convergence 188 setup time was (sec) 0.8000000 now iterating at: 17:03:48 rms-change max change #iterations 3.309822 151.6483 at 10iterations 1.383207 57.08891 at 20iterations 0.5824041 23.82162 at 30iterations 0.2457701 10.23710 at 40iterations 0.1029571 3.878880 at 50iterations 4.3363430E-02 1.700180 at 60iterations 1.8261483E-02 0.7209554 at 70iterations 7.6567139E-03 0.3002930 at 80iterations 3.2250765E-03 0.1250620 at 90iterations 1.3592499E-03 6.2281132E-02 at 100iterations 5.7321566E-04 2.0608425E-02 at 110iterations 2.4104750E-04 8.7037086E-03 at 120iterations finished qdiffx linear iterations at : 17:03:57 total time elapsed so far: 10.16000 # loops : 120 mean,max change (kT/e) : 2.4104750E-04 8.7037086E-03 energy calculations done at 10.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.33000 DelPhi exited at 17:03:59 10.332u 0.451s 0:12.69 84.9% 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 17:03:59 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 !!! WARNING: ASL 152 has a net charge of -0.1000 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 2.486960 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): 17.47000 64.88600 ymin,ymax (A): -9.516000 41.58700 zmin,zma (A): -1.976000 62.44000 x,y,z range (A): 47.41600 51.10300 64.41600 scale (grids/A): 2.486960 object centre (A): 41.17800 16.03550 30.23200 number of atom coordinates read : 2765 total number of charged atoms : 2622 net assigned charge : 5.806027 assigned positive charge : 409.5786 centred at (gu) : 92.21419 86.99488 86.65392 assigned negative charge : -403.7736 centred at (gu) : 92.14985 86.32572 86.77879 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 142130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25582 grid for indexing accessible points = 1.400000 m= 64701 mr = 99926 m= 18430 mr = 50202 m= 3179 mr = 13480 m= 210 mr = 2037 m= 3 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 261 time to turn everything in is 1.230000 number of dielectric boundary points 62930 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 20948 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) : 1.657973 object centre at (A) : 41.17800 16.03550 30.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2971513 0.4505998 midg,1,midg; midg,igrid,midg -6.1572388E-02 0.1510352 1,midg,midg; igrid,midg,midg 2.0943625E-02 5.6686597E-03 gauss-seidel spectral radius is 0.9991500 estimated iterations to convergence 271 setup time was (sec) 1.550000 now iterating at: 17:04:01 rms-change max change #iterations 8.557704 293.1257 at 10iterations 4.872764 176.7021 at 20iterations 2.754840 78.92750 at 30iterations 1.537952 41.23372 at 40iterations 0.8600581 21.08492 at 50iterations 0.4778393 10.05303 at 60iterations 0.2652896 6.587375 at 70iterations 0.1471217 3.310516 at 80iterations 8.1419826E-02 1.999808 at 90iterations 4.4991896E-02 0.9997692 at 100iterations 2.4858071E-02 0.5262184 at 110iterations 1.3726986E-02 0.2972975 at 120iterations 7.5741890E-03 0.1693192 at 130iterations 4.1812640E-03 9.5388412E-02 at 140iterations 2.3047742E-03 4.8416138E-02 at 150iterations 1.2715013E-03 2.6144028E-02 at 160iterations 7.0137152E-04 1.4307410E-02 at 170iterations 3.8634715E-04 8.6593628E-03 at 180iterations finished qdiffx linear iterations at : 17:04:17 total time elapsed so far: 16.97000 # loops : 180 mean,max change (kT/e) : 3.8634715E-04 8.6593628E-03 energy calculations done at 16.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.14000 DelPhi exited at 17:04:18 17.144u 0.464s 0:18.26 96.3% 0+0k 0+0io 0pf+0w