Mon Oct 10 16:58:03 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 Mon Oct 10 2011 at 16:58:03 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2884 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 0.5179914 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): -7.745000 39.64800 ymin,ymax (A): -9.229000 43.00100 zmin,zma (A): -3.204000 65.52300 x,y,z range (A): 47.39300 52.23000 68.72701 scale (grids/A): 0.5179914 object centre (A): 15.95150 16.88600 31.15950 number of atom coordinates read : 2884 total number of charged atoms : 2738 net assigned charge : 0.9060342 assigned positive charge : 430.3112 centred at (gu) : 90.88560 89.39442 88.54099 assigned negative charge : -429.4063 centred at (gu) : 90.83125 89.34074 88.65128 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5048 nv = 96 ne = 84 npr = 56579 no. pairs analyzed = 56579 no. exposed pairs = 4023 no. arc points = 28536 no. surface atoms = 1339 nbur = 1545 mkacc time = 9.9999994E-02 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 = 1.624000 m= 167 mr = 2358 m= 0 mr = 3 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2854 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2768 ## 429 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 6655 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6017581E-10 -1.5253669E-10 midg,1,midg; midg,igrid,midg -1.1879724E-10 1.0827771E-10 1,midg,midg; igrid,midg,midg -8.1071677E-11 1.6205437E-10 gauss-seidel spectral radius is 0.9808089 estimated iterations to convergence 60 setup time was (sec) 0.4100000 now iterating at: 16:58:04 rms-change max change #iterations 5.7558980E-02 10.79970 at 10iterations 3.2519656E-03 0.6620808 at 20iterations 2.1277762E-04 4.3136597E-02 at 30iterations 2.1305361E-05 4.0330887E-03 at 40iterations 3.3814556E-06 7.2765350E-04 at 50iterations finished qdiffx linear iterations at : 16:58:07 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 3.3814556E-06 7.2765350E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 16:58:07 3.468u 0.163s 0:04.06 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 Mon Oct 10 2011 at 16:58:07 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2884 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 1.553974 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): -7.745000 39.64800 ymin,ymax (A): -9.229000 43.00100 zmin,zma (A): -3.204000 65.52300 x,y,z range (A): 47.39300 52.23000 68.72701 scale (grids/A): 1.553974 object centre (A): 15.95150 16.88600 31.15950 number of atom coordinates read : 2884 total number of charged atoms : 2738 net assigned charge : 0.9060342 assigned positive charge : 430.3112 centred at (gu) : 92.65601 88.18237 85.62226 assigned negative charge : -429.4063 centred at (gu) : 92.49349 88.02197 85.95383 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 55951 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28536 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 15805 mr = 35899 m= 1309 mr = 10014 m= 24 mr = 480 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 26696 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 378 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 20661 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) : 0.5179914 object centre at (A) : 15.95150 16.88600 31.15950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3467913E-02 -7.1207951E-03 midg,1,midg; midg,igrid,midg -8.0379946E-03 -1.1363667E-03 1,midg,midg; igrid,midg,midg -1.0005186E-03 1.6637958E-03 gauss-seidel spectral radius is 0.9979844 estimated iterations to convergence 177 setup time was (sec) 0.5000000 now iterating at: 16:58:08 rms-change max change #iterations 2.904223 143.3404 at 10iterations 1.147229 53.60402 at 20iterations 0.4574281 20.79681 at 30iterations 0.1813800 7.235899 at 40iterations 7.2154224E-02 2.770683 at 50iterations 2.8702229E-02 1.080414 at 60iterations 1.1412170E-02 0.4766474 at 70iterations 4.5293272E-03 0.1780090 at 80iterations 1.8022056E-03 7.0259094E-02 at 90iterations 7.1838062E-04 2.7873039E-02 at 100iterations 2.8564050E-04 1.1093616E-02 at 110iterations 1.1426624E-04 4.6529770E-03 at 120iterations finished qdiffx linear iterations at : 16:58:15 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.1426624E-04 4.6529770E-03 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 16:58:16 7.690u 0.208s 0:08.24 95.7% 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 Mon Oct 10 2011 at 16:58:16 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2884 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 2.330961 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): -7.745000 39.64800 ymin,ymax (A): -9.229000 43.00100 zmin,zma (A): -3.204000 65.52300 x,y,z range (A): 47.39300 52.23000 68.72701 scale (grids/A): 2.330961 object centre (A): 15.95150 16.88600 31.15950 number of atom coordinates read : 2884 total number of charged atoms : 2738 net assigned charge : 0.9060342 assigned positive charge : 430.3112 centred at (gu) : 93.98383 87.27325 83.43316 assigned negative charge : -429.4063 centred at (gu) : 93.74004 87.03282 83.93066 start vw surface at 0.1000000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 130205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28536 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 56361 mr = 88788 m= 14198 mr = 42719 m= 1730 mr = 9841 m= 89 mr = 915 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 60308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 21860 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) : 1.553974 object centre at (A) : 15.95150 16.88600 31.15950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1349690 -0.1004338 midg,1,midg; midg,igrid,midg -0.1020777 -2.5839115E-02 1,midg,midg; igrid,midg,midg -9.0001132E-03 2.0949371E-02 gauss-seidel spectral radius is 0.9990776 estimated iterations to convergence 260 setup time was (sec) 0.9100000 now iterating at: 16:58:17 rms-change max change #iterations 7.891887 248.2640 at 10iterations 4.367746 130.9477 at 20iterations 2.390620 69.63378 at 30iterations 1.303756 30.38327 at 40iterations 0.7090238 20.72181 at 50iterations 0.3818992 9.786251 at 60iterations 0.2070095 4.789583 at 70iterations 0.1113567 2.632290 at 80iterations 5.9928093E-02 1.446415 at 90iterations 3.2353662E-02 0.7131538 at 100iterations 1.7409414E-02 0.3972158 at 110iterations 9.3636820E-03 0.2088470 at 120iterations 5.0253440E-03 0.1075897 at 130iterations 2.7001551E-03 5.8030128E-02 at 140iterations 1.4525355E-03 3.1954765E-02 at 150iterations 7.8126113E-04 1.7339706E-02 at 160iterations 4.2022488E-04 8.8348389E-03 at 170iterations 2.2642943E-04 5.3162575E-03 at 180iterations finished qdiffx linear iterations at : 16:58:28 total time elapsed so far: 12.09000 # loops : 180 mean,max change (kT/e) : 2.2642943E-04 5.3162575E-03 energy calculations done at 12.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.22000 DelPhi exited at 16:58:28 12.224u 0.205s 0:12.81 96.9% 0+0k 0+0io 0pf+0w