Sat Oct 8 23:48:13 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 23:48:13 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 = 3413 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5552869 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): -46.88300 7.271000 ymin,ymax (A): 176.7450 237.9000 zmin,zma (A): 78.67000 142.7810 x,y,z range (A): 54.15400 61.15500 64.11101 scale (grids/A): 0.5552869 object centre (A): -19.80600 207.3225 110.7255 number of atom coordinates read : 3413 total number of charged atoms : 3269 net assigned charge : 14.00002 assigned positive charge : 503.5814 centred at (gu) : 89.88502 89.30457 90.58547 assigned negative charge : -489.5832 centred at (gu) : 89.80302 89.23351 90.68871 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7107 nv = 96 ne = 84 npr = 66171 no. pairs analyzed = 66171 no. exposed pairs = 4647 no. arc points = 32537 no. surface atoms = 1547 nbur = 1866 mkacc time = 0.1100000 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 = 1.568000 m= 299 mr = 3527 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2300000 number of dielectric boundary points 3870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3298 ## 393 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9103 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0079507E-09 2.0373211E-10 midg,1,midg; midg,igrid,midg 6.1043870E-10 1.6823658E-09 1,midg,midg; igrid,midg,midg 4.1877088E-10 2.0407898E-09 gauss-seidel spectral radius is 0.9833201 estimated iterations to convergence 64 setup time was (sec) 0.4300000 now iterating at: 23:48:13 rms-change max change #iterations 8.5034773E-02 11.81181 at 10iterations 5.8903187E-03 0.9617004 at 20iterations 4.1836029E-04 6.6689014E-02 at 30iterations 3.4885201E-05 4.9996376E-03 at 40iterations 4.3137456E-06 5.9795380E-04 at 50iterations finished qdiffx linear iterations at : 23:48:16 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 4.3137456E-06 5.9795380E-04 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 23:48:17 3.418u 0.173s 0:03.93 91.0% 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 23:48:17 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 = 3413 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: 1.665861 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): -46.88300 7.271000 ymin,ymax (A): 176.7450 237.9000 zmin,zma (A): 78.67000 142.7810 x,y,z range (A): 54.15400 61.15500 64.11101 scale (grids/A): 1.665861 object centre (A): -19.80600 207.3225 110.7255 number of atom coordinates read : 3413 total number of charged atoms : 3269 net assigned charge : 14.00002 assigned positive charge : 503.5814 centred at (gu) : 89.65414 87.91286 91.75534 assigned negative charge : -489.5832 centred at (gu) : 89.40902 87.70020 92.06605 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32537 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24557 mr = 52001 m= 2622 mr = 16459 m= 83 mr = 1247 m= 0 mr = 7 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 911 time to turn everything in is 0.3800000 number of dielectric boundary points 35839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 332 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 25124 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) : 0.5552869 object centre at (A) : -19.80600 207.3225 110.7255 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2126630E-04 -5.7948614E-03 midg,1,midg; midg,igrid,midg 2.6136322E-02 2.6022160E-02 1,midg,midg; igrid,midg,midg 3.9753076E-03 1.6913923E-02 gauss-seidel spectral radius is 0.9983212 estimated iterations to convergence 194 setup time was (sec) 0.6000000 now iterating at: 23:48:17 rms-change max change #iterations 3.691007 187.1832 at 10iterations 1.582106 57.57544 at 20iterations 0.6807978 26.20718 at 30iterations 0.2928043 10.43359 at 40iterations 0.1260315 3.895168 at 50iterations 5.4152243E-02 1.770302 at 60iterations 2.3357047E-02 0.7769203 at 70iterations 1.0053385E-02 0.3357124 at 80iterations 4.3325825E-03 0.1351013 at 90iterations 1.8691819E-03 6.3076019E-02 at 100iterations 8.0716261E-04 2.5378227E-02 at 110iterations 3.4693134E-04 1.1749268E-02 at 120iterations finished qdiffx linear iterations at : 23:48:25 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 3.4693134E-04 1.1749268E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 23:48:25 7.773u 0.197s 0:08.29 96.0% 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 23:48:25 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 = 3413 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: 2.498791 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): -46.88300 7.271000 ymin,ymax (A): 176.7450 237.9000 zmin,zma (A): 78.67000 142.7810 x,y,z range (A): 54.15400 61.15500 64.11101 scale (grids/A): 2.498791 object centre (A): -19.80600 207.3225 110.7255 number of atom coordinates read : 3413 total number of charged atoms : 3269 net assigned charge : 14.00002 assigned positive charge : 503.5814 centred at (gu) : 89.48097 86.86906 92.63276 assigned negative charge : -489.5832 centred at (gu) : 89.11348 86.55025 93.09879 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 181889 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32537 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 83626 mr = 127877 m= 24667 mr = 64946 m= 4236 mr = 18233 m= 338 mr = 2700 m= 8 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 3241 time to turn everything in is 0.9300000 number of dielectric boundary points 80868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 26140 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) : 1.665861 object centre at (A) : -19.80600 207.3225 110.7255 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3684972 -7.7253714E-02 midg,1,midg; midg,igrid,midg 0.3472835 0.3905652 1,midg,midg; igrid,midg,midg -2.3093073E-04 0.1948433 gauss-seidel spectral radius is 0.9991985 estimated iterations to convergence 279 setup time was (sec) 1.170000 now iterating at: 23:48:27 rms-change max change #iterations 9.431478 279.3268 at 10iterations 5.458934 124.7871 at 20iterations 3.134770 71.70471 at 30iterations 1.788555 41.57565 at 40iterations 1.017758 21.51436 at 50iterations 0.5777948 12.49473 at 60iterations 0.3263718 6.445086 at 70iterations 0.1843621 3.684931 at 80iterations 0.1039859 1.999334 at 90iterations 5.8553476E-02 1.197845 at 100iterations 3.2913271E-02 0.6214676 at 110iterations 1.8506931E-02 0.3818531 at 120iterations 1.0409108E-02 0.1893082 at 130iterations 5.8390852E-03 0.1088448 at 140iterations 3.2909214E-03 6.7316055E-02 at 150iterations 1.8452858E-03 3.5705090E-02 at 160iterations 1.0376000E-03 1.8810272E-02 at 170iterations 5.8253581E-04 1.1019707E-02 at 180iterations finished qdiffx linear iterations at : 23:48:38 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 5.8253581E-04 1.1019707E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 23:48:38 12.651u 0.209s 0:13.17 97.5% 0+0k 0+0io 0pf+0w