Sat Oct 15 15:28:21 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 15:28:21 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 = 3834 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: 0.5431218 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): -13.87200 51.27100 ymin,ymax (A): 22.40000 87.94700 zmin,zma (A): 18.39300 77.30000 x,y,z range (A): 65.14300 65.54700 58.90701 scale (grids/A): 0.5431218 object centre (A): 18.69950 55.17350 47.84650 number of atom coordinates read : 3834 total number of charged atoms : 3677 net assigned charge : 9.500026 assigned positive charge : 585.0941 centred at (gu) : 89.42368 90.57197 92.69705 assigned negative charge : -575.5976 centred at (gu) : 89.44088 90.43063 92.82407 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7358 nv = 96 ne = 84 npr = 74571 no. pairs analyzed = 74571 no. exposed pairs = 5187 no. arc points = 37283 no. surface atoms = 1716 nbur = 2118 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 = 1.596000 m= 303 mr = 3543 m= 0 mr = 14 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4104 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3694 ## 545 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9610 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7607892E-10 -9.1577951E-10 midg,1,midg; midg,igrid,midg -4.7602750E-10 1.8546387E-09 1,midg,midg; igrid,midg,midg 7.8022683E-10 3.6160352E-10 gauss-seidel spectral radius is 0.9825969 estimated iterations to convergence 62 setup time was (sec) 0.5800000 now iterating at: 15:28:22 rms-change max change #iterations 8.2782254E-02 13.60697 at 10iterations 5.7253861E-03 0.9535828 at 20iterations 4.6179761E-04 8.5029602E-02 at 30iterations 6.6232147E-05 1.4308929E-02 at 40iterations 1.5350159E-05 2.7503967E-03 at 50iterations finished qdiffx linear iterations at : 15:28:25 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 1.5350159E-05 2.7503967E-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) 3.250000 DelPhi exited at 15:28:25 3.257u 0.204s 0:03.96 87.1% 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 15:28:25 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 = 3834 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: 1.629365 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): -13.87200 51.27100 ymin,ymax (A): 22.40000 87.94700 zmin,zma (A): 18.39300 77.30000 x,y,z range (A): 65.14300 65.54700 58.90701 scale (grids/A): 1.629365 object centre (A): 18.69950 55.17350 47.84650 number of atom coordinates read : 3834 total number of charged atoms : 3677 net assigned charge : 9.500026 assigned positive charge : 585.0941 centred at (gu) : 88.26943 91.71458 98.08994 assigned negative charge : -575.5976 centred at (gu) : 88.32225 91.29137 98.47160 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37283 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 24909 mr = 51135 m= 2810 mr = 16622 m= 84 mr = 1350 m= 0 mr = 8 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 134 time to turn everything in is 0.5800000 number of dielectric boundary points 38280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 470 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 28149 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) : 0.5431218 object centre at (A) : 18.69950 55.17350 47.84650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2816459E-02 -1.9516038E-03 midg,1,midg; midg,igrid,midg 6.1428170E-03 4.3301839E-02 1,midg,midg; igrid,midg,midg 1.6293678E-02 4.7524963E-03 gauss-seidel spectral radius is 0.9982706 estimated iterations to convergence 191 setup time was (sec) 0.8700000 now iterating at: 15:28:26 rms-change max change #iterations 3.831213 171.5162 at 10iterations 1.619746 54.19102 at 20iterations 0.6890581 23.12894 at 30iterations 0.2911724 9.822418 at 40iterations 0.1238864 4.448822 at 50iterations 5.2701216E-02 1.642321 at 60iterations 2.2497268E-02 0.7639771 at 70iterations 9.5665744E-03 0.3246422 at 80iterations 4.0726098E-03 0.1477470 at 90iterations 1.7403533E-03 5.6016922E-02 at 100iterations 7.4740703E-04 2.3648262E-02 at 110iterations 3.2323378E-04 1.0253906E-02 at 120iterations finished qdiffx linear iterations at : 15:28:33 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 3.2323378E-04 1.0253906E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 15:28:34 7.588u 0.237s 0:08.19 95.3% 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 15:28:34 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 = 3834 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: 2.444048 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): -13.87200 51.27100 ymin,ymax (A): 22.40000 87.94700 zmin,zma (A): 18.39300 77.30000 x,y,z range (A): 65.14300 65.54700 58.90701 scale (grids/A): 2.444048 object centre (A): 18.69950 55.17350 47.84650 number of atom coordinates read : 3834 total number of charged atoms : 3677 net assigned charge : 9.500026 assigned positive charge : 585.0941 centred at (gu) : 87.40372 92.57144 102.1347 assigned negative charge : -575.5976 centred at (gu) : 87.48343 91.93695 102.7074 start vw surface at 0.1900000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 184089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37283 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 84628 mr = 125878 m= 25567 mr = 65012 m= 4230 mr = 18813 m= 288 mr = 2725 m= 4 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 468 time to turn everything in is 1.420000 number of dielectric boundary points 86268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 29378 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) : 1.629365 object centre at (A) : 18.69950 55.17350 47.84650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1134640 -0.1145813 midg,1,midg; midg,igrid,midg 1.7283894E-02 0.7025409 1,midg,midg; igrid,midg,midg 9.6978769E-02 6.4856827E-02 gauss-seidel spectral radius is 0.9991879 estimated iterations to convergence 277 setup time was (sec) 1.730000 now iterating at: 15:28:36 rms-change max change #iterations 10.02583 305.3904 at 10iterations 5.749790 146.5687 at 20iterations 3.291299 72.93914 at 30iterations 1.868668 41.17953 at 40iterations 1.056814 21.09530 at 50iterations 0.5975614 12.82202 at 60iterations 0.3365645 6.885837 at 70iterations 0.1888337 3.691576 at 80iterations 0.1059651 2.203711 at 90iterations 5.9525672E-02 1.213318 at 100iterations 3.3357717E-02 0.7218494 at 110iterations 1.8716298E-02 0.3856697 at 120iterations 1.0476051E-02 0.1866150 at 130iterations 5.8690002E-03 0.1100330 at 140iterations 3.2898781E-03 6.4268589E-02 at 150iterations 1.8419874E-03 4.2676926E-02 at 160iterations 1.0317935E-03 2.1434784E-02 at 170iterations 5.8091362E-04 1.1262894E-02 at 180iterations finished qdiffx linear iterations at : 15:28:46 total time elapsed so far: 12.53000 # loops : 180 mean,max change (kT/e) : 5.8091362E-04 1.1262894E-02 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 15:28:47 12.708u 0.232s 0:13.44 96.2% 0+0k 0+0io 0pf+0w