Mon Oct 10 17:02:07 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 17:02:07 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2759 !!! WARNING: HIT 107 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5681275 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): -30.98300 31.67900 ymin,ymax (A): -23.89900 24.40200 zmin,zma (A): -46.64300 -1.312000 x,y,z range (A): 62.66200 48.30100 45.33100 scale (grids/A): 0.5681275 object centre (A): 0.3479996 0.2515001 -23.97750 number of atom coordinates read : 2759 total number of charged atoms : 2619 net assigned charge : 0.5140266 assigned positive charge : 418.5584 centred at (gu) : 90.38576 88.91248 89.82430 assigned negative charge : -418.0452 centred at (gu) : 90.26804 88.72233 89.66102 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5995 nv = 96 ne = 84 npr = 54275 no. pairs analyzed = 54275 no. exposed pairs = 3630 no. arc points = 25591 no. surface atoms = 1217 nbur = 1542 mkacc time = 8.9999996E-02 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 = 1.512000 m= 227 mr = 3020 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2000000 number of dielectric boundary points 3193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2579 ## 310 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7536 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2912594E-09 2.2267979E-09 midg,1,midg; midg,igrid,midg -3.3726559E-09 2.0622934E-09 1,midg,midg; igrid,midg,midg -1.4047219E-09 1.8826996E-09 gauss-seidel spectral radius is 0.9840032 estimated iterations to convergence 65 setup time was (sec) 0.3900000 now iterating at: 17:02:08 rms-change max change #iterations 8.8810444E-02 20.23068 at 10iterations 6.5740780E-03 1.089751 at 20iterations 4.8706098E-04 7.8404427E-02 at 30iterations 3.5909270E-05 6.1454773E-03 at 40iterations 2.6477483E-06 4.1961670E-04 at 50iterations finished qdiffx linear iterations at : 17:02:10 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.6477483E-06 4.1961670E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 17:02:12 3.418u 0.205s 0:05.00 72.2% 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 17:02:12 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2759 !!! WARNING: HIT 107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.704382 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): -30.98300 31.67900 ymin,ymax (A): -23.89900 24.40200 zmin,zma (A): -46.64300 -1.312000 x,y,z range (A): 62.66200 48.30100 45.33100 scale (grids/A): 1.704382 object centre (A): 0.3479996 0.2515001 -23.97750 number of atom coordinates read : 2759 total number of charged atoms : 2619 net assigned charge : 0.5140266 assigned positive charge : 418.5584 centred at (gu) : 91.15633 86.73661 89.47213 assigned negative charge : -418.0452 centred at (gu) : 90.80390 86.16688 88.98243 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 65366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25591 grid for indexing accessible points = 1.400000 m= 20412 mr = 43691 m= 2228 mr = 13792 m= 74 mr = 1083 m= 0 mr = 15 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 2164 time to turn everything in is 0.3200000 number of dielectric boundary points 29499 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 256 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20259 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) : 0.5681275 object centre at (A) : 0.3479996 0.2515001 -23.97750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7203135E-03 7.2781374E-03 midg,1,midg; midg,igrid,midg -2.7449267E-02 8.4747076E-03 1,midg,midg; igrid,midg,midg -9.8730670E-03 2.7787918E-02 gauss-seidel spectral radius is 0.9983226 estimated iterations to convergence 194 setup time was (sec) 0.5400000 now iterating at: 17:02:13 rms-change max change #iterations 3.566170 182.9213 at 10iterations 1.531241 63.56434 at 20iterations 0.6571231 24.09042 at 30iterations 0.2839367 10.34327 at 40iterations 0.1219851 4.407516 at 50iterations 5.2494250E-02 1.917523 at 60iterations 2.2667954E-02 0.7305164 at 70iterations 9.7368471E-03 0.3443556 at 80iterations 4.2069396E-03 0.1503143 at 90iterations 1.8174838E-03 6.3320160E-02 at 100iterations 7.7728846E-04 2.8873444E-02 at 110iterations 3.3742978E-04 1.3980865E-02 at 120iterations finished qdiffx linear iterations at : 17:02:20 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 3.3742978E-04 1.3980865E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 17:02:21 7.817u 0.211s 0:08.65 92.7% 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 17:02:21 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2759 !!! WARNING: HIT 107 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.556573 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): -30.98300 31.67900 ymin,ymax (A): -23.89900 24.40200 zmin,zma (A): -46.64300 -1.312000 x,y,z range (A): 62.66200 48.30100 45.33100 scale (grids/A): 2.556573 object centre (A): 0.3479996 0.2515001 -23.97750 number of atom coordinates read : 2759 total number of charged atoms : 2619 net assigned charge : 0.5140266 assigned positive charge : 418.5584 centred at (gu) : 91.73419 85.10476 89.20803 assigned negative charge : -418.0452 centred at (gu) : 91.20567 84.25011 88.47363 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 151842 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25591 grid for indexing accessible points = 1.400000 m= 69563 mr = 107053 m= 20510 mr = 54484 m= 3524 mr = 15282 m= 290 mr = 2266 m= 9 mr = 125 m= 0 mr = 5 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 6910 time to turn everything in is 0.7800000 number of dielectric boundary points 66523 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 20944 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) : 1.704382 object centre at (A) : 0.3479996 0.2515001 -23.97750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2210813E-02 8.5689120E-02 midg,1,midg; midg,igrid,midg -0.3583729 0.1280839 1,midg,midg; igrid,midg,midg 0.2318754 0.3031414 gauss-seidel spectral radius is 0.9991810 estimated iterations to convergence 276 setup time was (sec) 1.030000 now iterating at: 17:02:22 rms-change max change #iterations 9.032856 283.5094 at 10iterations 5.136643 125.2715 at 20iterations 2.902180 68.13120 at 30iterations 1.635632 36.20810 at 40iterations 0.9182990 19.93036 at 50iterations 0.5141245 11.45064 at 60iterations 0.2889375 6.170257 at 70iterations 0.1608424 3.573937 at 80iterations 9.0112545E-02 1.776753 at 90iterations 5.0281841E-02 1.010856 at 100iterations 2.8099269E-02 0.6740029 at 110iterations 1.5644060E-02 0.2968661 at 120iterations 8.7244231E-03 0.1632004 at 130iterations 4.8573450E-03 0.1004343 at 140iterations 2.7063347E-03 5.4224014E-02 at 150iterations 1.5076007E-03 2.9697418E-02 at 160iterations 8.4171596E-04 1.7854691E-02 at 170iterations 4.6838229E-04 9.3479156E-03 at 180iterations finished qdiffx linear iterations at : 17:02:33 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 4.6838229E-04 9.3479156E-03 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 17:02:34 12.483u 0.199s 0:13.31 95.1% 0+0k 0+0io 0pf+0w