Sat Oct 15 11:19:53 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 15 2011 at 11:19:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4461 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5041565 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): -2.694000 67.91900 ymin,ymax (A): -11.61900 39.14800 zmin,zma (A): -19.51300 46.06600 x,y,z range (A): 70.61300 50.76700 65.57899 scale (grids/A): 0.5041565 object centre (A): 32.61250 13.76450 13.27650 number of atom coordinates read : 4461 total number of charged atoms : 4306 net assigned charge : -5.499954 assigned positive charge : 672.9427 centred at (gu) : 88.07271 89.79435 90.50925 assigned negative charge : -678.4451 centred at (gu) : 88.14973 89.91801 90.56083 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7012 nv = 96 ne = 84 npr = 93874 no. pairs analyzed = 93874 no. exposed pairs = 4943 no. arc points = 33500 no. surface atoms = 1688 nbur = 2773 mkacc time = 0.1900000 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 = 1.680000 m= 241 mr = 3942 m= 0 mr = 13 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.4200000 number of dielectric boundary points 3298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3379 ## 514 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9515 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9461739E-11 -1.8025348E-10 midg,1,midg; midg,igrid,midg 1.7439317E-10 -2.7851826E-10 1,midg,midg; igrid,midg,midg 1.3878908E-10 -1.2335706E-10 gauss-seidel spectral radius is 0.9798474 estimated iterations to convergence 58 setup time was (sec) 0.6400000 now iterating at: 11:19:53 rms-change max change #iterations 5.9896313E-02 10.62713 at 10iterations 3.5859803E-03 0.5618706 at 20iterations 3.9422343E-04 6.2606812E-02 at 30iterations 8.3437160E-05 1.0378838E-02 at 40iterations 2.0096848E-05 2.6904345E-03 at 50iterations finished qdiffx linear iterations at : 11:19:56 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 2.0096848E-05 2.6904345E-03 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 11:19:56 3.271u 0.148s 0:03.70 92.1% 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 15 2011 at 11:19:56 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 = 4461 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.512469 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): -2.694000 67.91900 ymin,ymax (A): -11.61900 39.14800 zmin,zma (A): -19.51300 46.06600 x,y,z range (A): 70.61300 50.76700 65.57899 scale (grids/A): 1.512469 object centre (A): 32.61250 13.76450 13.27650 number of atom coordinates read : 4461 total number of charged atoms : 4306 net assigned charge : -5.499954 assigned positive charge : 672.9427 centred at (gu) : 84.21677 89.38167 91.52652 assigned negative charge : -678.4451 centred at (gu) : 84.44871 89.75372 91.68240 start vw surface at 0.1900000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33500 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23588 mr = 57650 m= 2023 mr = 16439 m= 26 mr = 934 m= 0 mr = 1 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2391 time to turn everything in is 0.5500000 number of dielectric boundary points 30613 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 475 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 32242 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) : 0.5041565 object centre at (A) : 32.61250 13.76450 13.27650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8952418E-03 -1.8269310E-02 midg,1,midg; midg,igrid,midg 2.1892712E-03 -9.9908551E-03 1,midg,midg; igrid,midg,midg 1.3859501E-02 -8.4496615E-03 gauss-seidel spectral radius is 0.9980024 estimated iterations to convergence 178 setup time was (sec) 0.8200000 now iterating at: 11:19:57 rms-change max change #iterations 3.537376 153.8186 at 10iterations 1.413137 50.74272 at 20iterations 0.5659453 21.60092 at 30iterations 0.2268353 7.321128 at 40iterations 9.0721332E-02 3.544923 at 50iterations 3.6511254E-02 1.239776 at 60iterations 1.4735389E-02 0.5881233 at 70iterations 5.9611858E-03 0.2000200 at 80iterations 2.4701592E-03 9.2144012E-02 at 90iterations 1.0532243E-03 3.4047127E-02 at 100iterations 4.7903677E-04 1.6870499E-02 at 110iterations 2.3650369E-04 7.7114105E-03 at 120iterations finished qdiffx linear iterations at : 11:20:03 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 2.3650369E-04 7.7114105E-03 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 11:20:04 7.012u 0.175s 0:07.69 93.3% 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 15 2011 at 11:20:04 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 = 4461 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.268704 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): -2.694000 67.91900 ymin,ymax (A): -11.61900 39.14800 zmin,zma (A): -19.51300 46.06600 x,y,z range (A): 70.61300 50.76700 65.57899 scale (grids/A): 2.268704 object centre (A): 32.61250 13.76450 13.27650 number of atom coordinates read : 4461 total number of charged atoms : 4306 net assigned charge : -5.499954 assigned positive charge : 672.9427 centred at (gu) : 81.32483 89.07243 92.28963 assigned negative charge : -678.4451 centred at (gu) : 81.67290 89.63039 92.52354 start vw surface at 0.2000000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 186869 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33500 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 85143 mr = 140849 m= 21827 mr = 68663 m= 2926 mr = 16402 m= 118 mr = 1811 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 7979 time to turn everything in is 1.300000 number of dielectric boundary points 69132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 34349 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) : 1.512469 object centre at (A) : 32.61250 13.76450 13.27650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1912649 -0.3817626 midg,1,midg; midg,igrid,midg 2.7390558E-02 -0.1619884 1,midg,midg; igrid,midg,midg 0.3203093 -0.5319053 gauss-seidel spectral radius is 0.9991058 estimated iterations to convergence 264 setup time was (sec) 1.590000 now iterating at: 11:20:06 rms-change max change #iterations 9.557725 344.5386 at 10iterations 5.337295 120.1050 at 20iterations 2.957710 73.99971 at 30iterations 1.632227 35.31334 at 40iterations 0.8987687 22.01961 at 50iterations 0.4932232 10.92848 at 60iterations 0.2694653 5.551870 at 70iterations 0.1474645 2.834440 at 80iterations 8.0405816E-02 1.622515 at 90iterations 4.3940473E-02 0.8244820 at 100iterations 2.4003973E-02 0.4451170 at 110iterations 1.3093213E-02 0.2569172 at 120iterations 7.1371868E-03 0.1518183 at 130iterations 3.9053478E-03 7.8821182E-02 at 140iterations 2.1424780E-03 4.3167114E-02 at 150iterations 1.1806905E-03 2.1730423E-02 at 160iterations 6.5960101E-04 1.4766693E-02 at 170iterations 3.7341722E-04 7.2313547E-03 at 180iterations finished qdiffx linear iterations at : 11:20:16 total time elapsed so far: 11.19000 # loops : 180 mean,max change (kT/e) : 3.7341722E-04 7.2313547E-03 energy calculations done at 11.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.36000 DelPhi exited at 11:20:16 11.361u 0.192s 0:12.11 95.3% 0+0k 0+0io 0pf+0w