Sat Oct 8 17:50:22 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+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 Sat Oct 8 2011 at 17:50:22 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3086 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: 0.5546727 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): -38.60200 10.66100 ymin,ymax (A): 8.614000 72.79600 zmin,zma (A): 61.66600 108.7530 x,y,z range (A): 49.26300 64.18200 47.08700 scale (grids/A): 0.5546727 object centre (A): -13.97050 40.70500 85.20950 number of atom coordinates read : 3086 total number of charged atoms : 2945 net assigned charge : 1.000005 assigned positive charge : 456.2291 centred at (gu) : 90.00906 89.11304 90.38527 assigned negative charge : -455.2302 centred at (gu) : 89.92190 89.07471 90.39043 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6322 nv = 96 ne = 84 npr = 62639 no. pairs analyzed = 62639 no. exposed pairs = 3758 no. arc points = 25913 no. surface atoms = 1274 nbur = 1812 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 = 1.540000 m= 275 mr = 3468 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2716 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8170 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2704911E-10 4.6621002E-11 midg,1,midg; midg,igrid,midg -3.3780986E-10 3.6105374E-10 1,midg,midg; igrid,midg,midg -7.3270667E-10 9.0092395E-10 gauss-seidel spectral radius is 0.9832442 estimated iterations to convergence 64 setup time was (sec) 0.4500000 now iterating at: 17:50:23 rms-change max change #iterations 8.1019945E-02 14.56893 at 10iterations 5.5715824E-03 0.9908628 at 20iterations 4.4705829E-04 7.0261002E-02 at 30iterations 6.3817271E-05 1.3292313E-02 at 40iterations 1.5701851E-05 3.5028458E-03 at 50iterations finished qdiffx linear iterations at : 17:50:26 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 1.5701851E-05 3.5028458E-03 energy calculations done at 3.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 17:50:27 3.936u 0.247s 0:04.44 93.9% 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 17:50:27 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3086 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: 1.664018 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): -38.60200 10.66100 ymin,ymax (A): 8.614000 72.79600 zmin,zma (A): 61.66600 108.7530 x,y,z range (A): 49.26300 64.18200 47.08700 scale (grids/A): 1.664018 object centre (A): -13.97050 40.70500 85.20950 number of atom coordinates read : 3086 total number of charged atoms : 2945 net assigned charge : 1.000005 assigned positive charge : 456.2291 centred at (gu) : 90.02636 87.33833 91.15503 assigned negative charge : -455.2302 centred at (gu) : 89.76530 87.22356 91.17094 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70117 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25913 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23774 mr = 49478 m= 2706 mr = 16919 m= 92 mr = 1440 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.3600000 number of dielectric boundary points 28842 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 0.4500000 number of grid points assigned charge 22654 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) : 0.5546727 object centre at (A) : -13.97050 40.70500 85.20950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4969334E-03 -4.1050706E-03 midg,1,midg; midg,igrid,midg 1.6032010E-02 -2.3904029E-02 1,midg,midg; igrid,midg,midg 4.0009897E-03 1.3535715E-02 gauss-seidel spectral radius is 0.9982645 estimated iterations to convergence 191 setup time was (sec) 0.6200000 now iterating at: 17:50:28 rms-change max change #iterations 3.519340 151.5133 at 10iterations 1.495667 53.47945 at 20iterations 0.6352406 26.67374 at 30iterations 0.2717583 9.656637 at 40iterations 0.1153948 4.029405 at 50iterations 4.9163096E-02 1.648105 at 60iterations 2.0931872E-02 0.8026047 at 70iterations 8.9453086E-03 0.3291969 at 80iterations 3.8197436E-03 0.1243896 at 90iterations 1.6332094E-03 5.6744576E-02 at 100iterations 6.9909339E-04 2.2712708E-02 at 110iterations 3.0366977E-04 1.0599613E-02 at 120iterations finished qdiffx linear iterations at : 17:50:36 total time elapsed so far: 8.930000 # loops : 120 mean,max change (kT/e) : 3.0366977E-04 1.0599613E-02 energy calculations done at 8.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.060000 DelPhi exited at 17:50:36 9.061u 0.293s 0:09.64 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 17:50:36 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3086 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: 2.496027 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): -38.60200 10.66100 ymin,ymax (A): 8.614000 72.79600 zmin,zma (A): 61.66600 108.7530 x,y,z range (A): 49.26300 64.18200 47.08700 scale (grids/A): 2.496027 object centre (A): -13.97050 40.70500 85.20950 number of atom coordinates read : 3086 total number of charged atoms : 2945 net assigned charge : 1.000005 assigned positive charge : 456.2291 centred at (gu) : 90.03943 86.00747 91.73222 assigned negative charge : -455.2302 centred at (gu) : 89.64780 85.83527 91.75623 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 162789 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25913 grid for indexing accessible points = 1.400000 m= 80751 mr = 120341 m= 24619 mr = 65341 m= 4390 mr = 18924 m= 392 mr = 2952 m= 4 mr = 191 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 126 time to turn everything in is 0.9100000 number of dielectric boundary points 65196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 23541 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) : 1.664018 object centre at (A) : -13.97050 40.70500 85.20950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1912594E-02 -4.8093315E-02 midg,1,midg; midg,igrid,midg 0.3614580 -0.4581022 1,midg,midg; igrid,midg,midg 8.3492748E-02 0.1872948 gauss-seidel spectral radius is 0.9991624 estimated iterations to convergence 273 setup time was (sec) 1.170000 now iterating at: 17:50:38 rms-change max change #iterations 8.910709 353.3654 at 10iterations 5.030385 141.1743 at 20iterations 2.822555 63.25933 at 30iterations 1.582477 32.87706 at 40iterations 0.8797188 19.08792 at 50iterations 0.4907379 9.865168 at 60iterations 0.2727645 5.367758 at 70iterations 0.1518243 2.933043 at 80iterations 8.4215380E-02 1.753311 at 90iterations 4.6777658E-02 1.060324 at 100iterations 2.5939448E-02 0.5104601 at 110iterations 1.4403291E-02 0.2699718 at 120iterations 7.9905977E-03 0.1544266 at 130iterations 4.4370671E-03 9.8114014E-02 at 140iterations 2.4650784E-03 4.7361374E-02 at 150iterations 1.3724118E-03 2.8306007E-02 at 160iterations 7.6682994E-04 1.5642643E-02 at 170iterations 4.3209386E-04 9.0637207E-03 at 180iterations finished qdiffx linear iterations at : 17:50:51 total time elapsed so far: 14.41000 # loops : 180 mean,max change (kT/e) : 4.3209386E-04 9.0637207E-03 energy calculations done at 14.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.54000 DelPhi exited at 17:50:51 14.538u 0.302s 0:15.11 98.1% 0+0k 0+0io 0pf+0w