Mon Oct 10 10:22:04 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 10:22:04 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2692 !!! WARNING: HIT 236 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5622503 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): -22.50800 40.80900 ymin,ymax (A): -11.49100 43.62600 zmin,zma (A): -1.435000 53.35600 x,y,z range (A): 63.31700 55.11700 54.79100 scale (grids/A): 0.5622503 object centre (A): 9.150500 16.06750 25.96050 number of atom coordinates read : 2692 total number of charged atoms : 2546 net assigned charge : 10.01403 assigned positive charge : 397.2461 centred at (gu) : 91.85821 91.14928 86.35837 assigned negative charge : -387.2325 centred at (gu) : 91.94780 91.16448 86.19208 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5659 nv = 96 ne = 84 npr = 52061 no. pairs analyzed = 52061 no. exposed pairs = 3974 no. arc points = 28816 no. surface atoms = 1324 nbur = 1368 mkacc time = 0.1200000 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= 291 mr = 2494 m= 0 mr = 10 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2798 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7217 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3835870E-09 1.2249740E-09 midg,1,midg; midg,igrid,midg 1.0538443E-09 1.3991588E-09 1,midg,midg; igrid,midg,midg 1.3715290E-09 4.3823564E-10 gauss-seidel spectral radius is 0.9836737 estimated iterations to convergence 64 setup time was (sec) 0.6000000 now iterating at: 10:22:05 rms-change max change #iterations 8.1440993E-02 15.20626 at 10iterations 5.7805437E-03 0.9478474 at 20iterations 4.2180624E-04 7.0504189E-02 at 30iterations 3.5774203E-05 5.3992271E-03 at 40iterations 4.4449703E-06 5.4740906E-04 at 50iterations finished qdiffx linear iterations at : 10:22:08 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 4.4449703E-06 5.4740906E-04 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 10:22:09 3.706u 0.201s 0:04.23 92.1% 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 Mon Oct 10 2011 at 10:22:09 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2692 !!! WARNING: HIT 236 has a net charge of 0.5140 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: 1.686751 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): -22.50800 40.80900 ymin,ymax (A): -11.49100 43.62600 zmin,zma (A): -1.435000 53.35600 x,y,z range (A): 63.31700 55.11700 54.79100 scale (grids/A): 1.686751 object centre (A): 9.150500 16.06750 25.96050 number of atom coordinates read : 2692 total number of charged atoms : 2546 net assigned charge : 10.01403 assigned positive charge : 397.2461 centred at (gu) : 95.57439 93.44747 79.07465 assigned negative charge : -387.2325 centred at (gu) : 95.84331 93.49341 78.57613 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 61256 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28816 grid for indexing accessible points = 1.400000 m= 18524 mr = 37527 m= 2099 mr = 11589 m= 72 mr = 874 m= 3 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.5100000 number of dielectric boundary points 31964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 276 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19675 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) : 0.5622503 object centre at (A) : 9.150500 16.06750 25.96050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4889724E-03 9.1496026E-03 midg,1,midg; midg,igrid,midg 1.6282810E-02 1.8521097E-02 1,midg,midg; igrid,midg,midg -1.3161593E-02 1.1270547E-02 gauss-seidel spectral radius is 0.9982774 estimated iterations to convergence 191 setup time was (sec) 0.8100000 now iterating at: 10:22:10 rms-change max change #iterations 3.313167 166.1489 at 10iterations 1.405602 57.07685 at 20iterations 0.5960771 23.10064 at 30iterations 0.2521225 9.069008 at 40iterations 0.1072724 4.109215 at 50iterations 4.5444570E-02 1.696938 at 60iterations 1.9288108E-02 0.6950111 at 70iterations 8.2261777E-03 0.2912350 at 80iterations 3.5067785E-03 0.1335630 at 90iterations 1.4896542E-03 5.2624226E-02 at 100iterations 6.3769886E-04 2.6816368E-02 at 110iterations 2.7158268E-04 1.1405945E-02 at 120iterations finished qdiffx linear iterations at : 10:22:17 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 2.7158268E-04 1.1405945E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.260000 DelPhi exited at 10:22:18 8.266u 0.285s 0:08.96 95.3% 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 10:22:18 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2692 !!! WARNING: HIT 236 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.530126 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): -22.50800 40.80900 ymin,ymax (A): -11.49100 43.62600 zmin,zma (A): -1.435000 53.35600 x,y,z range (A): 63.31700 55.11700 54.79100 scale (grids/A): 2.530126 object centre (A): 9.150500 16.06750 25.96050 number of atom coordinates read : 2692 total number of charged atoms : 2546 net assigned charge : 10.01403 assigned positive charge : 397.2461 centred at (gu) : 98.36153 95.17111 73.61195 assigned negative charge : -387.2325 centred at (gu) : 98.76492 95.23996 72.86409 start vw surface at 0.2100000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 141897 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28816 grid for indexing accessible points = 1.400000 m= 61917 mr = 92972 m= 18637 mr = 45896 m= 3173 mr = 13159 m= 262 mr = 1813 m= 7 mr = 73 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.6299999 no. cavity mid-points inaccessible to solvent = 146 time to turn everything in is 1.190000 number of dielectric boundary points 71980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 20349 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) : 1.686751 object centre at (A) : 9.150500 16.06750 25.96050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4693824E-02 0.1169565 midg,1,midg; midg,igrid,midg 0.2888874 0.2408888 1,midg,midg; igrid,midg,midg -0.5489278 0.1666977 gauss-seidel spectral radius is 0.9991629 estimated iterations to convergence 273 setup time was (sec) 1.490000 now iterating at: 10:22:19 rms-change max change #iterations 8.685295 258.5012 at 10iterations 5.027769 125.2225 at 20iterations 2.866215 82.17974 at 30iterations 1.618217 47.07419 at 40iterations 0.9133782 22.16660 at 50iterations 0.5120392 12.55714 at 60iterations 0.2864328 6.916157 at 70iterations 0.1599666 3.609995 at 80iterations 8.9266561E-02 2.720796 at 90iterations 4.9696788E-02 1.169585 at 100iterations 2.7579313E-02 0.6899939 at 110iterations 1.5370864E-02 0.3510075 at 120iterations 8.5224137E-03 0.1958241 at 130iterations 4.7303187E-03 0.1095371 at 140iterations 2.6248302E-03 5.7176590E-02 at 150iterations 1.4555173E-03 3.2371998E-02 at 160iterations 8.0748450E-04 1.7396927E-02 at 170iterations 4.4758164E-04 9.3655586E-03 at 180iterations finished qdiffx linear iterations at : 10:22:30 total time elapsed so far: 11.95000 # loops : 180 mean,max change (kT/e) : 4.4758164E-04 9.3655586E-03 energy calculations done at 11.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.15000 DelPhi exited at 10:22:30 12.152u 0.191s 0:12.66 97.4% 0+0k 0+0io 0pf+0w