Sun Oct 9 23:17:22 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 23:17:22 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 = 2259 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6695631 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): -12.14100 33.15300 ymin,ymax (A): -22.17700 28.11500 zmin,zma (A): -10.60500 42.56400 x,y,z range (A): 45.29400 50.29200 53.16900 scale (grids/A): 0.6695631 object centre (A): 10.50600 2.969000 15.97950 number of atom coordinates read : 2259 total number of charged atoms : 2120 net assigned charge : 2.500005 assigned positive charge : 333.5795 centred at (gu) : 91.50073 91.28077 90.50922 assigned negative charge : -331.0798 centred at (gu) : 91.47218 91.13669 90.24457 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7064 nv = 96 ne = 84 npr = 44128 no. pairs analyzed = 44128 no. exposed pairs = 2928 no. arc points = 20639 no. surface atoms = 993 nbur = 1266 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 3855 m= 3 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2700000 number of dielectric boundary points 3537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1848 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5685113E-08 6.9547447E-08 midg,1,midg; midg,igrid,midg -1.8225025E-08 4.9381491E-08 1,midg,midg; igrid,midg,midg 1.0369540E-09 1.8351491E-08 gauss-seidel spectral radius is 0.9884137 estimated iterations to convergence 76 setup time was (sec) 0.5100000 now iterating at: 23:17:23 rms-change max change #iterations 0.1608949 25.18168 at 10iterations 1.7725579E-02 2.718021 at 20iterations 1.9571818E-03 0.2616043 at 30iterations 2.4746294E-04 3.3191681E-02 at 40iterations 6.0942111E-05 1.1054754E-02 at 50iterations finished qdiffx linear iterations at : 23:17:26 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 6.0942111E-05 1.1054754E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 23:17:26 3.346u 0.204s 0:03.82 92.6% 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 23:17:26 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 = 2259 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.008689 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): -12.14100 33.15300 ymin,ymax (A): -22.17700 28.11500 zmin,zma (A): -10.60500 42.56400 x,y,z range (A): 45.29400 50.29200 53.16900 scale (grids/A): 2.008689 object centre (A): 10.50600 2.969000 15.97950 number of atom coordinates read : 2259 total number of charged atoms : 2120 net assigned charge : 2.500005 assigned positive charge : 333.5795 centred at (gu) : 94.50204 93.84207 91.52743 assigned negative charge : -331.0798 centred at (gu) : 94.41648 93.40991 90.73351 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 75923 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20639 grid for indexing accessible points = 1.400000 m= 27752 mr = 52231 m= 4660 mr = 20500 m= 353 mr = 3018 m= 5 mr = 183 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1269 time to turn everything in is 0.5300000 number of dielectric boundary points 32761 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 16787 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) : 0.6695631 object centre at (A) : 10.50600 2.969000 15.97950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9552056E-02 5.4876357E-03 midg,1,midg; midg,igrid,midg 1.7816612E-02 7.3535308E-02 1,midg,midg; igrid,midg,midg -1.4864281E-02 -9.7853178E-04 gauss-seidel spectral radius is 0.9987417 estimated iterations to convergence 223 setup time was (sec) 0.8200000 now iterating at: 23:17:27 rms-change max change #iterations 4.313990 185.2405 at 10iterations 2.076974 76.66952 at 20iterations 1.000628 33.92617 at 30iterations 0.4837981 15.37603 at 40iterations 0.2346009 6.825067 at 50iterations 0.1135904 3.156420 at 60iterations 5.4924637E-02 1.709361 at 70iterations 2.6480496E-02 0.8759613 at 80iterations 1.2867904E-02 0.4140167 at 90iterations 6.2946319E-03 0.1893435 at 100iterations 3.1246431E-03 0.1201839 at 110iterations 1.6024171E-03 5.1931381E-02 at 120iterations finished qdiffx linear iterations at : 23:17:34 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 1.6024171E-03 5.1931381E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 23:17:34 7.463u 0.244s 0:08.05 95.6% 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 23:17:34 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 = 2259 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.013034 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): -12.14100 33.15300 ymin,ymax (A): -22.17700 28.11500 zmin,zma (A): -10.60500 42.56400 x,y,z range (A): 45.29400 50.29200 53.16900 scale (grids/A): 3.013034 object centre (A): 10.50600 2.969000 15.97950 number of atom coordinates read : 2259 total number of charged atoms : 2120 net assigned charge : 2.500005 assigned positive charge : 333.5795 centred at (gu) : 96.75295 95.76288 92.29094 assigned negative charge : -331.0798 centred at (gu) : 96.62465 95.11478 91.10016 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 175331 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20639 grid for indexing accessible points = 1.400000 m= 89332 mr = 126302 m= 32751 mr = 73079 m= 8456 mr = 26454 m= 1562 mr = 6560 m= 158 mr = 1147 m= 5 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.8100001 no. cavity mid-points inaccessible to solvent = 3899 time to turn everything in is 1.360000 number of dielectric boundary points 73941 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 16960 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) : 2.008689 object centre at (A) : 10.50600 2.969000 15.97950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5975268 -0.1134749 midg,1,midg; midg,igrid,midg 0.2096901 0.7566344 1,midg,midg; igrid,midg,midg -0.2017165 8.9519966E-04 gauss-seidel spectral radius is 0.9992883 estimated iterations to convergence 296 setup time was (sec) 1.670000 now iterating at: 23:17:36 rms-change max change #iterations 9.992802 330.6691 at 10iterations 5.896131 147.8808 at 20iterations 3.473416 73.56271 at 30iterations 2.041578 41.86306 at 40iterations 1.198885 23.86451 at 50iterations 0.7011347 13.05038 at 60iterations 0.4088754 7.781036 at 70iterations 0.2388010 4.544590 at 80iterations 0.1392789 2.580746 at 90iterations 8.1058688E-02 1.500999 at 100iterations 4.7229841E-02 0.8561935 at 110iterations 2.7498294E-02 0.4854958 at 120iterations 1.6009517E-02 0.2978973 at 130iterations 9.3243578E-03 0.1579552 at 140iterations 5.4245694E-03 9.8084450E-02 at 150iterations 3.1523996E-03 5.8254242E-02 at 160iterations 1.8315571E-03 3.1221390E-02 at 170iterations 1.0653718E-03 1.8686295E-02 at 180iterations finished qdiffx linear iterations at : 23:17:47 total time elapsed so far: 11.98000 # loops : 180 mean,max change (kT/e) : 1.0653718E-03 1.8686295E-02 energy calculations done at 11.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.17000 DelPhi exited at 23:17:47 12.175u 0.227s 0:12.67 97.7% 0+0k 0+0io 0pf+0w