Sun Oct 9 15:49:26 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 15:49:26 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 = 5432 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: 0.5071008 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): -17.59700 52.60600 ymin,ymax (A): 93.83900 160.9660 zmin,zma (A): -32.28200 34.53300 x,y,z range (A): 70.20300 67.12701 66.81499 scale (grids/A): 0.5071008 object centre (A): 17.50450 127.4025 1.125500 number of atom coordinates read : 5432 total number of charged atoms : 5261 net assigned charge : 3.2767653E-05 assigned positive charge : 833.0557 centred at (gu) : 89.17609 88.39527 89.10187 assigned negative charge : -833.0629 centred at (gu) : 89.18363 88.43089 89.02318 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8584 nv = 96 ne = 84 npr = 110657 no. pairs analyzed = 110657 no. exposed pairs = 6446 no. arc points = 44924 no. surface atoms = 2154 nbur = 3278 mkacc time = 0.1900000 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= 287 mr = 4553 m= 3 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4333 ## 650 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 11641 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6242014E-10 1.5873898E-10 midg,1,midg; midg,igrid,midg 1.4241970E-10 -6.0267430E-11 1,midg,midg; igrid,midg,midg 2.4673976E-11 -1.5482752E-11 gauss-seidel spectral radius is 0.9801500 estimated iterations to convergence 59 setup time was (sec) 0.5700000 now iterating at: 15:49:27 rms-change max change #iterations 6.8490162E-02 11.77557 at 10iterations 6.3747088E-03 0.9754677 at 20iterations 2.0508608E-03 0.3559341 at 30iterations 7.9343002E-04 0.1400299 at 40iterations 3.0690336E-04 5.4576874E-02 at 50iterations finished qdiffx linear iterations at : 15:49:30 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 3.0690336E-04 5.4576874E-02 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 15:49:31 3.645u 0.157s 0:04.19 90.4% 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 15:49:31 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 = 5432 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: 1.521302 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): -17.59700 52.60600 ymin,ymax (A): 93.83900 160.9660 zmin,zma (A): -32.28200 34.53300 x,y,z range (A): 70.20300 67.12701 66.81499 scale (grids/A): 1.521302 object centre (A): 17.50450 127.4025 1.125500 number of atom coordinates read : 5432 total number of charged atoms : 5261 net assigned charge : 3.2767653E-05 assigned positive charge : 833.0557 centred at (gu) : 87.52656 85.18417 87.30370 assigned negative charge : -833.0629 centred at (gu) : 87.55053 85.29230 87.06934 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 97983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44924 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 28515 mr = 68701 m= 2404 mr = 19115 m= 48 mr = 935 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 820 time to turn everything in is 0.4800000 number of dielectric boundary points 40199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 536 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 39335 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) : 0.5071008 object centre at (A) : 17.50450 127.4025 1.125500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0629452E-02 2.9735619E-03 midg,1,midg; midg,igrid,midg 1.5845239E-02 -2.0829080E-04 1,midg,midg; igrid,midg,midg -2.7258482E-02 -1.2329323E-03 gauss-seidel spectral radius is 0.9981234 estimated iterations to convergence 183 setup time was (sec) 0.7000000 now iterating at: 15:49:31 rms-change max change #iterations 4.064532 176.4080 at 10iterations 1.665132 53.42059 at 20iterations 0.6857849 20.82571 at 30iterations 0.2837011 8.806997 at 40iterations 0.1170070 3.560680 at 50iterations 4.8598401E-02 1.503502 at 60iterations 2.0711632E-02 0.6704865 at 70iterations 9.2298789E-03 0.2985802 at 80iterations 4.5447275E-03 0.1677828 at 90iterations 2.5850595E-03 9.5283508E-02 at 100iterations 1.6482919E-03 6.2334061E-02 at 110iterations 1.1239180E-03 4.3191910E-02 at 120iterations finished qdiffx linear iterations at : 15:49:39 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 1.1239180E-03 4.3191910E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 15:49:39 8.070u 0.229s 0:08.61 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 Sun Oct 9 2011 at 15:49:39 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 = 5432 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: 2.281954 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): -17.59700 52.60600 ymin,ymax (A): 93.83900 160.9660 zmin,zma (A): -32.28200 34.53300 x,y,z range (A): 70.20300 67.12701 66.81499 scale (grids/A): 2.281954 object centre (A): 17.50450 127.4025 1.125500 number of atom coordinates read : 5432 total number of charged atoms : 5261 net assigned charge : 3.2767653E-05 assigned positive charge : 833.0557 centred at (gu) : 86.28954 82.77571 85.95500 assigned negative charge : -833.0629 centred at (gu) : 86.32578 82.93837 85.60409 start vw surface at 0.1300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 228833 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44924 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 102312 mr = 168857 m= 25979 mr = 80259 m= 3409 mr = 18727 m= 169 mr = 1979 m= 4 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 2927 time to turn everything in is 1.160000 number of dielectric boundary points 90848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 41988 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) : 1.521302 object centre at (A) : 17.50450 127.4025 1.125500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1727626 0.1061791 midg,1,midg; midg,igrid,midg 0.2648188 -4.5390472E-02 1,midg,midg; igrid,midg,midg -0.7030808 2.8613260E-02 gauss-seidel spectral radius is 0.9991680 estimated iterations to convergence 274 setup time was (sec) 1.400000 now iterating at: 15:49:41 rms-change max change #iterations 10.94531 277.9307 at 10iterations 6.269641 152.8790 at 20iterations 3.549477 96.87468 at 30iterations 2.007201 45.04930 at 40iterations 1.128083 23.39987 at 50iterations 0.6334837 12.23041 at 60iterations 0.3547011 7.142963 at 70iterations 0.1981581 3.790598 at 80iterations 0.1107938 2.037496 at 90iterations 6.1888691E-02 1.118777 at 100iterations 3.4538046E-02 0.6586876 at 110iterations 1.9281238E-02 0.3291817 at 120iterations 1.0795726E-02 0.1971245 at 130iterations 6.0795713E-03 0.1125221 at 140iterations 3.4591528E-03 6.0998917E-02 at 150iterations 2.0114668E-03 3.4986496E-02 at 160iterations 1.2150413E-03 2.4868011E-02 at 170iterations 7.7298930E-04 1.6006470E-02 at 180iterations finished qdiffx linear iterations at : 15:49:53 total time elapsed so far: 13.07000 # loops : 180 mean,max change (kT/e) : 7.7298930E-04 1.6006470E-02 energy calculations done at 13.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.20000 DelPhi exited at 15:49:53 13.206u 0.227s 0:13.73 97.7% 0+0k 0+0io 0pf+0w