Sat Oct 8 11:37:15 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 Sat Oct 8 2011 at 11:37:15 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 = 2548 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: 0.5749354 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): -10.48000 37.23600 ymin,ymax (A): -34.30800 27.61200 zmin,zma (A): -13.97400 39.46300 x,y,z range (A): 47.71600 61.92000 53.43700 scale (grids/A): 0.5749354 object centre (A): 13.37800 -3.348001 12.74450 number of atom coordinates read : 2548 total number of charged atoms : 2398 net assigned charge : -2.999991 assigned positive charge : 369.6139 centred at (gu) : 90.14237 90.81738 91.63349 assigned negative charge : -372.6144 centred at (gu) : 90.10468 90.87575 91.55349 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5510 nv = 96 ne = 84 npr = 51424 no. pairs analyzed = 51424 no. exposed pairs = 3387 no. arc points = 23849 no. surface atoms = 1147 nbur = 1401 mkacc time = 0.1300000 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 = 1.484000 m= 231 mr = 2745 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2345 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7027 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2377771E-09 1.0100458E-09 midg,1,midg; midg,igrid,midg 2.7427038E-10 -1.7895754E-09 1,midg,midg; igrid,midg,midg -1.1116273E-09 2.2984002E-11 gauss-seidel spectral radius is 0.9843572 estimated iterations to convergence 66 setup time was (sec) 0.6100000 now iterating at: 11:37:16 rms-change max change #iterations 8.7192297E-02 15.70426 at 10iterations 6.6304975E-03 1.104765 at 20iterations 4.9940415E-04 8.2397461E-02 at 30iterations 3.9850751E-05 5.7690144E-03 at 40iterations 3.3439569E-06 5.7601929E-04 at 50iterations finished qdiffx linear iterations at : 11:37:21 total time elapsed so far: 5.640000 # loops : 50 mean,max change (kT/e) : 3.3439569E-06 5.7601929E-04 energy calculations done at 5.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.860000 DelPhi exited at 11:37:22 5.860u 0.472s 0:07.10 89.1% 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 Sat Oct 8 2011 at 11:37:22 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 = 2548 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: 1.724806 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): -10.48000 37.23600 ymin,ymax (A): -34.30800 27.61200 zmin,zma (A): -13.97400 39.46300 x,y,z range (A): 47.71600 61.92000 53.43700 scale (grids/A): 1.724806 object centre (A): 13.37800 -3.348001 12.74450 number of atom coordinates read : 2548 total number of charged atoms : 2398 net assigned charge : -2.999991 assigned positive charge : 369.6139 centred at (gu) : 90.42648 92.45155 94.89977 assigned negative charge : -372.6144 centred at (gu) : 90.31384 92.62688 94.66040 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 60752 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23849 grid for indexing accessible points = 1.400000 m= 18658 mr = 40068 m= 2023 mr = 12717 m= 83 mr = 1031 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 156 time to turn everything in is 0.6400000 number of dielectric boundary points 27692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 218 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 18575 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) : 0.5749354 object centre at (A) : 13.37800 -3.348001 12.74450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0986964E-02 8.0960263E-03 midg,1,midg; midg,igrid,midg -2.2003209E-05 -2.1838028E-02 1,midg,midg; igrid,midg,midg -8.3317058E-03 3.6962233E-03 gauss-seidel spectral radius is 0.9983369 estimated iterations to convergence 195 setup time was (sec) 1.200000 now iterating at: 11:37:24 rms-change max change #iterations 3.378564 186.4620 at 10iterations 1.457292 63.69374 at 20iterations 0.6285601 22.26667 at 30iterations 0.2721559 10.32520 at 40iterations 0.1172294 4.274197 at 50iterations 5.0705019E-02 1.924538 at 60iterations 2.1888671E-02 0.7997704 at 70iterations 9.4886711E-03 0.3267841 at 80iterations 4.1098860E-03 0.1693802 at 90iterations 1.7782850E-03 6.7106515E-02 at 100iterations 7.7224994E-04 2.8239250E-02 at 110iterations 3.3416273E-04 1.1592865E-02 at 120iterations finished qdiffx linear iterations at : 11:37:41 total time elapsed so far: 17.99000 # loops : 120 mean,max change (kT/e) : 3.3416273E-04 1.1592865E-02 energy calculations done at 17.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.19000 DelPhi exited at 11:37:42 18.190u 0.816s 0:19.59 96.9% 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 Sat Oct 8 2011 at 11:37:42 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 = 2548 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: 2.587209 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): -10.48000 37.23600 ymin,ymax (A): -34.30800 27.61200 zmin,zma (A): -13.97400 39.46300 x,y,z range (A): 47.71600 61.92000 53.43700 scale (grids/A): 2.587209 object centre (A): 13.37800 -3.348001 12.74450 number of atom coordinates read : 2548 total number of charged atoms : 2398 net assigned charge : -2.999991 assigned positive charge : 369.6139 centred at (gu) : 90.63952 93.67701 97.34960 assigned negative charge : -372.6144 centred at (gu) : 90.47076 93.94031 96.99063 start vw surface at 0.1300000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 140981 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23849 grid for indexing accessible points = 1.400000 m= 63758 mr = 98163 m= 18757 mr = 49972 m= 3267 mr = 14061 m= 235 mr = 2159 m= 3 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 571 time to turn everything in is 1.570000 number of dielectric boundary points 62554 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 19172 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) : 1.724806 object centre at (A) : 13.37800 -3.348001 12.74450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1502569 0.1768905 midg,1,midg; midg,igrid,midg 8.2675017E-02 -0.6227184 1,midg,midg; igrid,midg,midg -0.1208911 7.3768772E-02 gauss-seidel spectral radius is 0.9991747 estimated iterations to convergence 275 setup time was (sec) 2.060000 now iterating at: 11:37:45 rms-change max change #iterations 8.530327 358.3721 at 10iterations 4.854290 149.7863 at 20iterations 2.747508 65.14215 at 30iterations 1.546135 35.14460 at 40iterations 0.8712052 19.42681 at 50iterations 0.4876838 11.17749 at 60iterations 0.2732210 6.606529 at 70iterations 0.1529703 4.121029 at 80iterations 8.5487537E-02 1.821892 at 90iterations 4.7681898E-02 1.089462 at 100iterations 2.6495675E-02 0.7028680 at 110iterations 1.4803495E-02 0.3005829 at 120iterations 8.2453564E-03 0.2062073 at 130iterations 4.6001663E-03 9.3548775E-02 at 140iterations 2.5665122E-03 5.6964874E-02 at 150iterations 1.4317866E-03 3.1173706E-02 at 160iterations 8.0035243E-04 1.9334674E-02 at 170iterations 4.4817678E-04 9.0322495E-03 at 180iterations finished qdiffx linear iterations at : 11:38:14 total time elapsed so far: 31.19000 # loops : 180 mean,max change (kT/e) : 4.4817678E-04 9.0322495E-03 energy calculations done at 31.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 31.39000 DelPhi exited at 11:38:14 31.396u 0.781s 0:32.60 98.6% 0+0k 0+0io 0pf+0w