Sun Oct 9 19:39:06 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 19:39:06 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5424 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5097657 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): 3.241000 68.24300 ymin,ymax (A): -9.058000 53.24500 zmin,zma (A): -2.568000 67.26800 x,y,z range (A): 65.00201 62.30300 69.83600 scale (grids/A): 0.5097657 object centre (A): 35.74200 22.09350 32.35000 number of atom coordinates read : 5424 total number of charged atoms : 5253 net assigned charge : 3.621032 assigned positive charge : 831.4247 centred at (gu) : 88.17670 89.39931 89.09326 assigned negative charge : -827.8100 centred at (gu) : 88.08379 89.42502 89.01684 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8934 nv = 96 ne = 84 npr = 110565 no. pairs analyzed = 110565 no. exposed pairs = 6203 no. arc points = 42549 no. surface atoms = 2117 nbur = 3307 mkacc time = 0.2600000 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 = 1.680000 m= 309 mr = 4989 m= 0 mr = 6 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4248 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4245 ## 601 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 11992 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1263682E-10 2.1617108E-10 midg,1,midg; midg,igrid,midg 1.5296023E-10 -1.4807698E-11 1,midg,midg; igrid,midg,midg -3.5370504E-10 1.9878565E-10 gauss-seidel spectral radius is 0.9803574 estimated iterations to convergence 59 setup time was (sec) 0.7800000 now iterating at: 19:39:07 rms-change max change #iterations 7.5062171E-02 11.39964 at 10iterations 7.5896941E-03 1.122337 at 20iterations 2.7292764E-03 0.3515749 at 30iterations 1.2652883E-03 0.1807070 at 40iterations 6.0595211E-04 8.9256287E-02 at 50iterations finished qdiffx linear iterations at : 19:39:10 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 6.0595211E-04 8.9256287E-02 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 19:39:10 3.735u 0.145s 0:04.27 90.6% 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 19:39:11 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5424 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.529297 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): 3.241000 68.24300 ymin,ymax (A): -9.058000 53.24500 zmin,zma (A): -2.568000 67.26800 x,y,z range (A): 65.00201 62.30300 69.83600 scale (grids/A): 1.529297 object centre (A): 35.74200 22.09350 32.35000 number of atom coordinates read : 5424 total number of charged atoms : 5253 net assigned charge : 3.621032 assigned positive charge : 831.4247 centred at (gu) : 84.52876 88.19651 87.27776 assigned negative charge : -827.8100 centred at (gu) : 84.25073 88.27477 87.05038 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 101782 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42549 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 31932 mr = 73217 m= 2949 mr = 22329 m= 57 mr = 1321 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 39853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 585 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 39472 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) : 0.5097657 object centre at (A) : 35.74200 22.09350 32.35000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4805561E-02 1.8573171E-02 midg,1,midg; midg,igrid,midg 1.3247534E-02 5.2912496E-03 1,midg,midg; igrid,midg,midg -1.3267433E-02 5.8318754E-03 gauss-seidel spectral radius is 0.9981484 estimated iterations to convergence 185 setup time was (sec) 1.030000 now iterating at: 19:39:12 rms-change max change #iterations 4.154511 179.4253 at 10iterations 1.717572 56.96693 at 20iterations 0.7126332 21.46498 at 30iterations 0.2943521 8.327133 at 40iterations 0.1226474 3.459011 at 50iterations 5.1573750E-02 1.544542 at 60iterations 2.2112165E-02 0.6273956 at 70iterations 1.0126982E-02 0.3356934 at 80iterations 5.3248657E-03 0.1667976 at 90iterations 3.2914195E-03 9.4646454E-02 at 100iterations 2.3029465E-03 6.2961102E-02 at 110iterations 1.6996575E-03 4.7176361E-02 at 120iterations finished qdiffx linear iterations at : 19:39:18 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 1.6996575E-03 4.7176361E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 19:39:19 7.671u 0.167s 0:08.23 95.1% 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 19:39:19 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5424 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.293946 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): 3.241000 68.24300 ymin,ymax (A): -9.058000 53.24500 zmin,zma (A): -2.568000 67.26800 x,y,z range (A): 65.00201 62.30300 69.83600 scale (grids/A): 2.293946 object centre (A): 35.74200 22.09350 32.35000 number of atom coordinates read : 5424 total number of charged atoms : 5253 net assigned charge : 3.621032 assigned positive charge : 831.4247 centred at (gu) : 81.79263 87.29449 85.91631 assigned negative charge : -827.8100 centred at (gu) : 81.37590 87.41221 85.57558 start vw surface at 0.2200000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 237240 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42549 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 112518 mr = 178799 m= 30675 mr = 90546 m= 4345 mr = 22981 m= 229 mr = 2666 m= 2 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.840000 number of dielectric boundary points 89940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 41885 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) : 1.529297 object centre at (A) : 35.74200 22.09350 32.35000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2813669 0.6529424 midg,1,midg; midg,igrid,midg 0.2032134 3.9327826E-02 1,midg,midg; igrid,midg,midg -0.3147906 9.9196412E-02 gauss-seidel spectral radius is 0.9991742 estimated iterations to convergence 275 setup time was (sec) 2.170000 now iterating at: 19:39:21 rms-change max change #iterations 10.99313 263.8498 at 10iterations 6.293454 140.9140 at 20iterations 3.564430 70.37537 at 30iterations 2.017313 39.31389 at 40iterations 1.136873 21.46730 at 50iterations 0.6371815 12.11526 at 60iterations 0.3574601 6.640617 at 70iterations 0.2004698 3.625122 at 80iterations 0.1124808 2.033203 at 90iterations 6.2965095E-02 1.091650 at 100iterations 3.5368904E-02 0.6376686 at 110iterations 2.0040771E-02 0.3639011 at 120iterations 1.1545680E-02 0.2152290 at 130iterations 6.8428465E-03 0.1342163 at 140iterations 4.2727683E-03 8.2093790E-02 at 150iterations 2.8822429E-03 6.0492516E-02 at 160iterations 2.1014113E-03 3.8346291E-02 at 170iterations 1.6262918E-03 2.7642250E-02 at 180iterations finished qdiffx linear iterations at : 19:39:32 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 1.6262918E-03 2.7642250E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 19:39:32 12.755u 0.180s 0:13.24 97.6% 0+0k 0+0io 0pf+0w