Thu Jan 19 11:42:37 PST 2012 #!/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 Thu Jan 19 2012 at 11:42:38 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5133 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4918418 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): -35.93500 25.64700 ymin,ymax (A): -12.42000 55.71900 zmin,zma (A): 2.376000 74.75700 x,y,z range (A): 61.58200 68.13900 72.38100 scale (grids/A): 0.4918418 object centre (A): -5.144001 21.64950 38.56650 number of atom coordinates read : 5133 total number of charged atoms : 4960 net assigned charge : 23.99995 assigned positive charge : 786.8184 centred at (gu) : 90.53063 91.36513 90.80901 assigned negative charge : -762.8244 centred at (gu) : 90.46005 91.37994 90.83566 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7868 nv = 96 ne = 84 npr = 100446 no. pairs analyzed = 100446 no. exposed pairs = 6437 no. arc points = 44374 no. surface atoms = 2163 nbur = 2970 mkacc time = 0.2600000 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 = 1.736000 m= 255 mr = 4034 m= 0 mr = 4 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4308 ## 706 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 10619 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4066802E-10 1.3661788E-10 midg,1,midg; midg,igrid,midg 1.1173566E-10 1.7927305E-10 1,midg,midg; igrid,midg,midg 4.9938869E-11 2.6149988E-10 gauss-seidel spectral radius is 0.9788961 estimated iterations to convergence 57 setup time was (sec) 0.8500000 now iterating at: 11:42:39 rms-change max change #iterations 5.6802921E-02 10.02448 at 10iterations 4.1698976E-03 0.5652046 at 20iterations 1.2171629E-03 9.9428177E-02 at 30iterations 4.8504383E-04 3.9886475E-02 at 40iterations 1.9577218E-04 1.6207695E-02 at 50iterations finished qdiffx linear iterations at : 11:42:44 total time elapsed so far: 5.550000 # loops : 50 mean,max change (kT/e) : 1.9577218E-04 1.6207695E-02 energy calculations done at 5.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.720000 DelPhi exited at 11:42:44 5.729u 0.422s 0:06.92 88.7% 0+0k 0+0io 6pf+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 Thu Jan 19 2012 at 11:42:45 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5133 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.475525 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): -35.93500 25.64700 ymin,ymax (A): -12.42000 55.71900 zmin,zma (A): 2.376000 74.75700 x,y,z range (A): 61.58200 68.13900 72.38100 scale (grids/A): 1.475525 object centre (A): -5.144001 21.64950 38.56650 number of atom coordinates read : 5133 total number of charged atoms : 4960 net assigned charge : 23.99995 assigned positive charge : 786.8184 centred at (gu) : 91.59068 94.09367 92.42540 assigned negative charge : -762.8244 centred at (gu) : 91.38003 94.13952 92.50700 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 90899 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44374 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 24714 mr = 62558 m= 1583 mr = 15944 m= 22 mr = 464 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 2427 time to turn everything in is 0.7800000 number of dielectric boundary points 38252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 697 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 36764 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) : 0.4918418 object centre at (A) : -5.144001 21.64950 38.56650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7052062E-03 2.5786445E-04 midg,1,midg; midg,igrid,midg -5.2071264E-04 6.2125665E-03 1,midg,midg; igrid,midg,midg 8.7893698E-03 2.1484153E-02 gauss-seidel spectral radius is 0.9979845 estimated iterations to convergence 177 setup time was (sec) 1.110000 now iterating at: 11:42:46 rms-change max change #iterations 3.648901 171.3298 at 10iterations 1.451974 49.16784 at 20iterations 0.5805189 19.13171 at 30iterations 0.2323772 7.842501 at 40iterations 9.2921682E-02 3.414833 at 50iterations 3.7327774E-02 1.252937 at 60iterations 1.5136618E-02 0.4581070 at 70iterations 6.3381782E-03 0.2085800 at 80iterations 2.8281694E-03 9.1724396E-02 at 90iterations 1.4449244E-03 3.9367676E-02 at 100iterations 8.5967372E-04 2.4147034E-02 at 110iterations 5.6853285E-04 1.2233734E-02 at 120iterations finished qdiffx linear iterations at : 11:42:58 total time elapsed so far: 12.97000 # loops : 120 mean,max change (kT/e) : 5.6853285E-04 1.2233734E-02 energy calculations done at 12.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 11:42:59 13.154u 0.519s 0:14.19 96.2% 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 Thu Jan 19 2012 at 11:42:59 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5133 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.213288 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): -35.93500 25.64700 ymin,ymax (A): -12.42000 55.71900 zmin,zma (A): 2.376000 74.75700 x,y,z range (A): 61.58200 68.13900 72.38100 scale (grids/A): 2.213288 object centre (A): -5.144001 21.64950 38.56650 number of atom coordinates read : 5133 total number of charged atoms : 4960 net assigned charge : 23.99995 assigned positive charge : 786.8184 centred at (gu) : 92.38552 96.14021 93.63758 assigned negative charge : -762.8244 centred at (gu) : 92.07019 96.20920 93.76038 start vw surface at 0.1800000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 212293 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44374 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 92305 mr = 154119 m= 19506 mr = 71569 m= 1892 mr = 13258 m= 59 mr = 904 m= 0 mr = 5 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 8346 time to turn everything in is 1.840000 number of dielectric boundary points 86200 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 39533 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) : 1.475525 object centre at (A) : -5.144001 21.64950 38.56650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2029466 3.1060154E-02 midg,1,midg; midg,igrid,midg -5.0326549E-02 -9.9764541E-02 1,midg,midg; igrid,midg,midg 0.1364887 0.3518237 gauss-seidel spectral radius is 0.9991416 estimated iterations to convergence 270 setup time was (sec) 2.220000 now iterating at: 11:43:02 rms-change max change #iterations 10.18771 310.6528 at 10iterations 5.815878 174.8177 at 20iterations 3.302183 82.89102 at 30iterations 1.868131 41.43791 at 40iterations 1.053867 23.66188 at 50iterations 0.5915729 12.99383 at 60iterations 0.3319330 7.503250 at 70iterations 0.1858954 3.717044 at 80iterations 0.1038327 2.370827 at 90iterations 5.7837106E-02 1.136819 at 100iterations 3.2189973E-02 0.6253510 at 110iterations 1.7923098E-02 0.3699865 at 120iterations 9.9590262E-03 0.1950989 at 130iterations 5.5426322E-03 0.1162148 at 140iterations 3.0877851E-03 5.9780121E-02 at 150iterations 1.7202864E-03 3.4145355E-02 at 160iterations 9.6115033E-04 2.0832300E-02 at 170iterations 5.4241804E-04 1.1634827E-02 at 180iterations finished qdiffx linear iterations at : 11:43:21 total time elapsed so far: 21.49000 # loops : 180 mean,max change (kT/e) : 5.4241804E-04 1.1634827E-02 energy calculations done at 21.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.65000 DelPhi exited at 11:43:22 21.652u 0.530s 0:22.78 97.3% 0+0k 0+0io 0pf+0w