Sun Oct 9 15:56:17 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 15:56:17 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 = 5331 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.4994669 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): -103.7540 -32.47800 ymin,ymax (A): -56.55900 9.970000 zmin,zma (A): -30.49500 37.05100 x,y,z range (A): 71.27600 66.52900 67.54601 scale (grids/A): 0.4994669 object centre (A): -68.11600 -23.29450 3.278001 number of atom coordinates read : 5331 total number of charged atoms : 5159 net assigned charge : -1.499958 assigned positive charge : 814.5525 centred at (gu) : 89.06012 89.18651 89.13222 assigned negative charge : -816.0593 centred at (gu) : 89.03551 89.26363 89.06923 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8219 nv = 96 ne = 84 npr = 108541 no. pairs analyzed = 108541 no. exposed pairs = 6252 no. arc points = 43333 no. surface atoms = 2090 nbur = 3241 mkacc time = 0.2700000 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= 275 mr = 4417 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.5300000 number of dielectric boundary points 4067 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4100 ## 625 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 11059 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6219477E-10 7.9773195E-11 midg,1,midg; midg,igrid,midg 1.5803812E-10 -1.2362929E-10 1,midg,midg; igrid,midg,midg -7.4024176E-11 2.4812933E-11 gauss-seidel spectral radius is 0.9795340 estimated iterations to convergence 58 setup time was (sec) 0.7700000 now iterating at: 15:56:18 rms-change max change #iterations 6.2708691E-02 9.908937 at 10iterations 5.7899537E-03 1.122107 at 20iterations 1.8669437E-03 0.3678589 at 30iterations 7.2236446E-04 0.1423798 at 40iterations 2.7876321E-04 5.5130005E-02 at 50iterations finished qdiffx linear iterations at : 15:56:21 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 2.7876321E-04 5.5130005E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 15:56:21 3.604u 0.148s 0:04.03 92.8% 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 15:56:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5331 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.498401 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): -103.7540 -32.47800 ymin,ymax (A): -56.55900 9.970000 zmin,zma (A): -30.49500 37.05100 x,y,z range (A): 71.27600 66.52900 67.54601 scale (grids/A): 1.498401 object centre (A): -68.11600 -23.29450 3.278001 number of atom coordinates read : 5331 total number of charged atoms : 5159 net assigned charge : -1.499958 assigned positive charge : 814.5525 centred at (gu) : 87.17894 87.55832 87.39484 assigned negative charge : -816.0593 centred at (gu) : 87.10593 87.79092 87.20769 start vw surface at 0.2300000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 94301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43333 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27065 mr = 66553 m= 2270 mr = 18372 m= 42 mr = 905 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 3032 time to turn everything in is 0.7000000 number of dielectric boundary points 37848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 547 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 38362 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) : 0.4994669 object centre at (A) : -68.11600 -23.29450 3.278001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2922486E-03 5.0310865E-03 midg,1,midg; midg,igrid,midg 1.4356608E-02 -9.2026358E-03 1,midg,midg; igrid,midg,midg -3.2240029E-02 4.6219197E-03 gauss-seidel spectral radius is 0.9980553 estimated iterations to convergence 180 setup time was (sec) 1.000000 now iterating at: 15:56:23 rms-change max change #iterations 3.877186 152.5755 at 10iterations 1.572259 51.63976 at 20iterations 0.6387285 20.46137 at 30iterations 0.2591064 8.994039 at 40iterations 0.1052153 3.284260 at 50iterations 4.2954210E-02 1.355513 at 60iterations 1.7961910E-02 0.6395340 at 70iterations 7.8494940E-03 0.3279305 at 80iterations 3.7724646E-03 0.1402435 at 90iterations 2.1237722E-03 9.3055725E-02 at 100iterations 1.3452596E-03 5.4786682E-02 at 110iterations 9.1714668E-04 3.8379669E-02 at 120iterations finished qdiffx linear iterations at : 15:56:29 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 9.1714668E-04 3.8379669E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 15:56:30 8.043u 0.158s 0:08.52 96.1% 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 Sun Oct 9 2011 at 15:56:30 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 = 5331 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.247601 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): -103.7540 -32.47800 ymin,ymax (A): -56.55900 9.970000 zmin,zma (A): -30.49500 37.05100 x,y,z range (A): 71.27600 66.52900 67.54601 scale (grids/A): 2.247601 object centre (A): -68.11600 -23.29450 3.278001 number of atom coordinates read : 5331 total number of charged atoms : 5159 net assigned charge : -1.499958 assigned positive charge : 814.5525 centred at (gu) : 85.76803 86.33715 86.09201 assigned negative charge : -816.0593 centred at (gu) : 85.65891 86.68642 85.81145 start vw surface at 0.2200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 220214 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43333 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 97985 mr = 163433 m= 24279 mr = 77412 m= 3252 mr = 17686 m= 154 mr = 1881 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 10438 time to turn everything in is 1.640000 number of dielectric boundary points 85438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 41138 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) : 1.498401 object centre at (A) : -68.11600 -23.29450 3.278001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7745828E-02 9.8528177E-02 midg,1,midg; midg,igrid,midg 0.3619381 -0.1308698 1,midg,midg; igrid,midg,midg -0.7641612 0.1288916 gauss-seidel spectral radius is 0.9991484 estimated iterations to convergence 271 setup time was (sec) 1.950000 now iterating at: 15:56:32 rms-change max change #iterations 10.60251 244.7384 at 10iterations 6.027006 170.7475 at 20iterations 3.389800 91.77824 at 30iterations 1.904782 41.48596 at 40iterations 1.061993 24.51665 at 50iterations 0.5932863 15.74865 at 60iterations 0.3303666 6.596466 at 70iterations 0.1831158 3.744217 at 80iterations 0.1018407 1.773544 at 90iterations 5.6326035E-02 1.078627 at 100iterations 3.1341560E-02 0.5457611 at 110iterations 1.7337337E-02 0.3367577 at 120iterations 9.6510649E-03 0.1717420 at 130iterations 5.4023364E-03 9.9822998E-02 at 140iterations 3.0628128E-03 6.5196991E-02 at 150iterations 1.7669953E-03 3.5644531E-02 at 160iterations 1.0590567E-03 2.2989273E-02 at 170iterations 6.7057641E-04 1.5563965E-02 at 180iterations finished qdiffx linear iterations at : 15:56:43 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 6.7057641E-04 1.5563965E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 15:56:43 12.745u 0.188s 0:13.34 96.8% 0+0k 0+0io 0pf+0w