Sun Oct 9 03:04:41 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 Sun Oct 9 2011 at 03:04:41 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4584 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.4454789 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): -2.876000 77.03800 ymin,ymax (A): 0.6680001 67.46799 zmin,zma (A): 167.5620 228.5290 x,y,z range (A): 79.91400 66.80000 60.96698 scale (grids/A): 0.4454789 object centre (A): 37.08100 34.06800 198.0455 number of atom coordinates read : 4584 total number of charged atoms : 4350 net assigned charge : 19.00001 assigned positive charge : 671.3860 centred at (gu) : 86.03088 91.04752 88.66135 assigned negative charge : -652.3907 centred at (gu) : 85.97807 90.99812 88.68639 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5440 nv = 96 ne = 84 npr = 93822 no. pairs analyzed = 93822 no. exposed pairs = 5718 no. arc points = 39388 no. surface atoms = 1957 nbur = 2627 mkacc time = 0.1600000 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 = 1.904000 m= 147 mr = 2632 m= 0 mr = 1 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3379 ## 688 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7416 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7764295E-11 4.9216434E-12 midg,1,midg; midg,igrid,midg 3.6459741E-12 1.9423706E-11 1,midg,midg; igrid,midg,midg 1.4091452E-11 4.6234154E-12 gauss-seidel spectral radius is 0.9742781 estimated iterations to convergence 52 setup time was (sec) 0.5000000 now iterating at: 03:04:41 rms-change max change #iterations 3.3672802E-02 8.215187 at 10iterations 2.6576589E-03 0.4895325 at 20iterations 4.6611310E-04 8.8512421E-02 at 30iterations 9.0013578E-05 1.6883850E-02 at 40iterations 1.7504426E-05 3.2615662E-03 at 50iterations finished qdiffx linear iterations at : 03:04:44 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 1.7504426E-05 3.2615662E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 03:04:45 3.600u 0.230s 0:04.31 88.8% 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 03:04:45 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4584 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.336437 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): -2.876000 77.03800 ymin,ymax (A): 0.6680001 67.46799 zmin,zma (A): 167.5620 228.5290 x,y,z range (A): 79.91400 66.80000 60.96698 scale (grids/A): 1.336437 object centre (A): 37.08100 34.06800 198.0455 number of atom coordinates read : 4584 total number of charged atoms : 4350 net assigned charge : 19.00001 assigned positive charge : 671.3860 centred at (gu) : 78.09088 93.14088 85.98238 assigned negative charge : -652.3907 centred at (gu) : 77.93404 92.99416 86.05923 start vw surface at 0.1300000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 63205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39388 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 15196 mr = 41986 m= 780 mr = 9347 m= 7 mr = 175 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 895 time to turn everything in is 0.3500000 number of dielectric boundary points 27680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 660 ## 19 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 30813 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) : 0.4454789 object centre at (A) : 37.08100 34.06800 198.0455 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2432882E-03 8.0388965E-04 midg,1,midg; midg,igrid,midg 2.4482668E-03 3.6140524E-03 1,midg,midg; igrid,midg,midg 2.2176711E-02 3.2854807E-03 gauss-seidel spectral radius is 0.9973849 estimated iterations to convergence 156 setup time was (sec) 0.5600000 now iterating at: 03:04:46 rms-change max change #iterations 2.566118 128.8446 at 10iterations 0.8946309 36.80040 at 20iterations 0.3151473 12.41056 at 30iterations 0.1111413 4.594528 at 40iterations 3.9201010E-02 1.573003 at 50iterations 1.4082228E-02 0.5110044 at 60iterations 5.2268356E-03 0.2057533 at 70iterations 2.0649219E-03 7.8756332E-02 at 80iterations 9.0610143E-04 3.5015106E-02 at 90iterations 4.4206777E-04 1.4322281E-02 at 100iterations 2.3419733E-04 8.1672668E-03 at 110iterations 1.2872432E-04 3.9215088E-03 at 120iterations finished qdiffx linear iterations at : 03:04:53 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 1.2872432E-04 3.9215088E-03 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 03:04:53 7.671u 0.227s 0:08.28 95.2% 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 Sun Oct 9 2011 at 03:04:53 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4584 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.004655 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): -2.876000 77.03800 ymin,ymax (A): 0.6680001 67.46799 zmin,zma (A): 167.5620 228.5290 x,y,z range (A): 79.91400 66.80000 60.96698 scale (grids/A): 2.004655 object centre (A): 37.08100 34.06800 198.0455 number of atom coordinates read : 4584 total number of charged atoms : 4350 net assigned charge : 19.00001 assigned positive charge : 671.3860 centred at (gu) : 72.13584 94.71096 83.97321 assigned negative charge : -652.3907 centred at (gu) : 71.90096 94.49105 84.08855 start vw surface at 0.1000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 148083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39388 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 58408 mr = 104589 m= 11253 mr = 43715 m= 926 mr = 7399 m= 17 mr = 394 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 3179 time to turn everything in is 0.7300000 number of dielectric boundary points 62590 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 34458 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) : 1.336437 object centre at (A) : 37.08100 34.06800 198.0455 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1802703E-02 1.2429669E-02 midg,1,midg; midg,igrid,midg 5.0207913E-02 6.3003868E-02 1,midg,midg; igrid,midg,midg 0.5049120 4.0015023E-02 gauss-seidel spectral radius is 0.9988996 estimated iterations to convergence 239 setup time was (sec) 0.9700000 now iterating at: 03:04:55 rms-change max change #iterations 7.654140 221.9535 at 10iterations 4.003923 111.6441 at 20iterations 2.086802 51.66224 at 30iterations 1.078786 27.12199 at 40iterations 0.5576159 13.59679 at 50iterations 0.2868024 7.903893 at 60iterations 0.1470940 3.851915 at 70iterations 7.5338639E-02 1.797525 at 80iterations 3.8561247E-02 0.8118019 at 90iterations 1.9716389E-02 0.4673576 at 100iterations 1.0072398E-02 0.2339716 at 110iterations 5.1576942E-03 0.1203456 at 120iterations 2.6371130E-03 5.9692383E-02 at 130iterations 1.3579337E-03 3.1145096E-02 at 140iterations 7.0096529E-04 1.5579224E-02 at 150iterations 3.6648879E-04 8.3446503E-03 at 160iterations 1.9423846E-04 4.2505264E-03 at 170iterations 1.0504441E-04 2.3632050E-03 at 180iterations finished qdiffx linear iterations at : 03:05:07 total time elapsed so far: 12.27000 # loops : 180 mean,max change (kT/e) : 1.0504441E-04 2.3632050E-03 energy calculations done at 12.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 03:05:08 12.415u 1.508s 0:14.21 97.8% 0+0k 0+0io 0pf+0w