Sun Oct 9 03:29:16 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 Sun Oct 9 2011 at 03:29:16 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4238 !!! WARNING: HIZ 388 has a net charge of 0.2000 !!! WARNING: HEM 601 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5408115 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): -3.499000 54.18600 ymin,ymax (A): 17.77000 83.59700 zmin,zma (A): -18.22600 44.93500 x,y,z range (A): 57.68500 65.82700 63.16100 scale (grids/A): 0.5408115 object centre (A): 25.34350 50.68350 13.35450 number of atom coordinates read : 4238 total number of charged atoms : 4047 net assigned charge : 12.10003 assigned positive charge : 622.4365 centred at (gu) : 90.21808 92.14168 90.15485 assigned negative charge : -610.3410 centred at (gu) : 90.25162 92.13311 90.14031 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7907 nv = 96 ne = 84 npr = 86701 no. pairs analyzed = 86701 no. exposed pairs = 5263 no. arc points = 36915 no. surface atoms = 1799 nbur = 2439 mkacc time = 0.1500000 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 = 1.568000 m= 350 mr = 4125 m= 0 mr = 17 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4115 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3619 ## 443 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 10471 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8268201E-10 7.4555728E-10 midg,1,midg; midg,igrid,midg 3.2777281E-10 1.1418472E-09 1,midg,midg; igrid,midg,midg 8.1415041E-10 3.7694628E-10 gauss-seidel spectral radius is 0.9824733 estimated iterations to convergence 62 setup time was (sec) 0.4900000 now iterating at: 03:29:17 rms-change max change #iterations 8.3751105E-02 12.29918 at 10iterations 7.3131775E-03 1.043450 at 20iterations 1.4634886E-03 0.1857986 at 30iterations 4.3858399E-04 5.3573608E-02 at 40iterations 1.3515702E-04 1.6279221E-02 at 50iterations finished qdiffx linear iterations at : 03:29:20 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 1.3515702E-04 1.6279221E-02 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 03:29:20 3.581u 0.191s 0:04.06 92.8% 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 Sun Oct 9 2011 at 03:29:20 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4238 !!! WARNING: HIZ 388 has a net charge of 0.2000 !!! WARNING: HEM 601 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.622435 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): -3.499000 54.18600 ymin,ymax (A): 17.77000 83.59700 zmin,zma (A): -18.22600 44.93500 x,y,z range (A): 57.68500 65.82700 63.16100 scale (grids/A): 1.622435 object centre (A): 25.34350 50.68350 13.35450 number of atom coordinates read : 4238 total number of charged atoms : 4047 net assigned charge : 12.10003 assigned positive charge : 622.4365 centred at (gu) : 90.65289 96.42324 90.46305 assigned negative charge : -610.3410 centred at (gu) : 90.75460 96.39912 90.42093 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 88071 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36915 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 27571 mr = 59994 m= 2928 mr = 19017 m= 83 mr = 1450 m= 0 mr = 5 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 946 time to turn everything in is 0.4500000 number of dielectric boundary points 38187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 389 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 30958 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) : 0.5408115 object centre at (A) : 25.34350 50.68350 13.35450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9545622E-02 7.3982351E-03 midg,1,midg; midg,igrid,midg 1.3458068E-02 2.3521511E-02 1,midg,midg; igrid,midg,midg 3.5410800E-03 -2.6615614E-03 gauss-seidel spectral radius is 0.9982976 estimated iterations to convergence 192 setup time was (sec) 0.7100000 now iterating at: 03:29:21 rms-change max change #iterations 3.978392 166.4256 at 10iterations 1.701086 63.66998 at 20iterations 0.7304286 23.80453 at 30iterations 0.3126031 11.09485 at 40iterations 0.1345353 5.310699 at 50iterations 5.7966232E-02 1.733124 at 60iterations 2.5175393E-02 0.8088188 at 70iterations 1.0977486E-02 0.3539658 at 80iterations 4.9223187E-03 0.1569366 at 90iterations 2.3128318E-03 7.2460175E-02 at 100iterations 1.1456811E-03 3.8553298E-02 at 110iterations 6.2233879E-04 1.8520355E-02 at 120iterations finished qdiffx linear iterations at : 03:29:29 total time elapsed so far: 8.710000 # loops : 120 mean,max change (kT/e) : 6.2233879E-04 1.8520355E-02 energy calculations done at 8.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.860000 DelPhi exited at 03:29:30 8.860u 0.244s 0:09.43 96.5% 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 Sun Oct 9 2011 at 03:29:30 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4238 !!! WARNING: HIZ 388 has a net charge of 0.2000 !!! WARNING: HEM 601 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.433652 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): -3.499000 54.18600 ymin,ymax (A): 17.77000 83.59700 zmin,zma (A): -18.22600 44.93500 x,y,z range (A): 57.68500 65.82700 63.16100 scale (grids/A): 2.433652 object centre (A): 25.34350 50.68350 13.35450 number of atom coordinates read : 4238 total number of charged atoms : 4047 net assigned charge : 12.10003 assigned positive charge : 622.4365 centred at (gu) : 90.97903 99.63438 90.69415 assigned negative charge : -610.3410 centred at (gu) : 91.13193 99.59872 90.63113 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 204891 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36915 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 94561 mr = 147201 m= 27695 mr = 74622 m= 4486 mr = 20895 m= 281 mr = 2958 m= 2 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.5999999 no. cavity mid-points inaccessible to solvent = 3117 time to turn everything in is 1.080000 number of dielectric boundary points 86132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 32347 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) : 1.622435 object centre at (A) : 25.34350 50.68350 13.35450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1937543 2.3169976E-02 midg,1,midg; midg,igrid,midg 0.1751935 0.2213242 1,midg,midg; igrid,midg,midg 2.0277677E-03 5.9221130E-02 gauss-seidel spectral radius is 0.9992049 estimated iterations to convergence 280 setup time was (sec) 1.340000 now iterating at: 03:29:31 rms-change max change #iterations 10.32081 340.7761 at 10iterations 5.985372 130.3391 at 20iterations 3.447058 80.19089 at 30iterations 1.978270 38.36166 at 40iterations 1.130406 20.68167 at 50iterations 0.6411738 12.54177 at 60iterations 0.3650534 6.997796 at 70iterations 0.2067796 3.997471 at 80iterations 0.1168309 2.042557 at 90iterations 6.6247188E-02 1.142746 at 100iterations 3.7501361E-02 0.6823101 at 110iterations 2.1222796E-02 0.3605194 at 120iterations 1.2052827E-02 0.2216034 at 130iterations 6.8471190E-03 0.1271572 at 140iterations 3.9238092E-03 7.1559906E-02 at 150iterations 2.2769670E-03 4.1317940E-02 at 160iterations 1.3399844E-03 2.4538040E-02 at 170iterations 8.1391720E-04 1.6201019E-02 at 180iterations finished qdiffx linear iterations at : 03:29:44 total time elapsed so far: 13.76000 # loops : 180 mean,max change (kT/e) : 8.1391720E-04 1.6201019E-02 energy calculations done at 13.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.89000 DelPhi exited at 03:29:44 13.887u 0.238s 0:14.40 97.9% 0+0k 0+0io 0pf+0w