Tue Oct 11 03:14:26 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 Tue Oct 11 2011 at 03:14:26 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 = 3166 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: 0.5342938 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): -11.15500 39.56800 ymin,ymax (A): 67.34299 127.0350 zmin,zma (A): 106.0880 172.7180 x,y,z range (A): 50.72300 59.69201 66.63000 scale (grids/A): 0.5342938 object centre (A): 14.20650 97.18900 139.4030 number of atom coordinates read : 3166 total number of charged atoms : 3027 net assigned charge : -5.999976 assigned positive charge : 471.9338 centred at (gu) : 88.80264 91.49075 93.03486 assigned negative charge : -477.9349 centred at (gu) : 88.84666 91.48260 93.06118 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5694 nv = 96 ne = 84 npr = 65591 no. pairs analyzed = 65591 no. exposed pairs = 3907 no. arc points = 27401 no. surface atoms = 1315 nbur = 1851 mkacc time = 0.1400000 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= 215 mr = 2969 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2777 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7653 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5688683E-11 -7.5153495E-10 midg,1,midg; midg,igrid,midg -1.8484685E-10 -2.7782293E-10 1,midg,midg; igrid,midg,midg -4.0379047E-11 -3.1800979E-10 gauss-seidel spectral radius is 0.9819573 estimated iterations to convergence 61 setup time was (sec) 0.5600000 now iterating at: 03:14:27 rms-change max change #iterations 6.8884291E-02 15.97771 at 10iterations 4.3974067E-03 0.7199249 at 20iterations 3.2375124E-04 5.6351662E-02 at 30iterations 3.9945946E-05 7.5675845E-03 at 40iterations 7.5816347E-06 1.5786439E-03 at 50iterations finished qdiffx linear iterations at : 03:14:29 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 7.5816347E-06 1.5786439E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 03:14:30 3.348u 0.206s 0:04.02 88.0% 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 Tue Oct 11 2011 at 03:14:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3166 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: 1.602881 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): -11.15500 39.56800 ymin,ymax (A): 67.34299 127.0350 zmin,zma (A): 106.0880 172.7180 x,y,z range (A): 50.72300 59.69201 66.63000 scale (grids/A): 1.602881 object centre (A): 14.20650 97.18900 139.4030 number of atom coordinates read : 3166 total number of charged atoms : 3027 net assigned charge : -5.999976 assigned positive charge : 471.9338 centred at (gu) : 86.40734 94.47169 99.10363 assigned negative charge : -477.9349 centred at (gu) : 86.53967 94.44716 99.18334 start vw surface at 0.1900000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 63282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27401 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19012 mr = 42753 m= 1817 mr = 13174 m= 39 mr = 869 m= 0 mr = 4 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 275 time to turn everything in is 0.4900000 number of dielectric boundary points 27350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 373 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 23058 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) : 0.5342938 object centre at (A) : 14.20650 97.18900 139.4030 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3565808E-02 -1.2988735E-02 midg,1,midg; midg,igrid,midg -3.3920542E-03 3.6964663E-03 1,midg,midg; igrid,midg,midg -2.9281694E-03 -5.7565123E-03 gauss-seidel spectral radius is 0.9981190 estimated iterations to convergence 183 setup time was (sec) 0.7700000 now iterating at: 03:14:31 rms-change max change #iterations 3.285640 150.3937 at 10iterations 1.344239 53.09921 at 20iterations 0.5533539 21.49205 at 30iterations 0.2271335 7.810095 at 40iterations 9.3745396E-02 3.326617 at 50iterations 3.8475432E-02 1.302824 at 60iterations 1.5798394E-02 0.6040361 at 70iterations 6.4909081E-03 0.2565174 at 80iterations 2.6724548E-03 9.2208862E-02 at 90iterations 1.1066536E-03 4.2209022E-02 at 100iterations 4.5998098E-04 1.8177986E-02 at 110iterations 1.9352714E-04 6.9446564E-03 at 120iterations finished qdiffx linear iterations at : 03:14:37 total time elapsed so far: 7.170000 # loops : 120 mean,max change (kT/e) : 1.9352714E-04 6.9446564E-03 energy calculations done at 7.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.330000 DelPhi exited at 03:14:38 7.336u 0.235s 0:08.00 94.5% 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 Tue Oct 11 2011 at 03:14:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3166 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: 2.404322 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): -11.15500 39.56800 ymin,ymax (A): 67.34299 127.0350 zmin,zma (A): 106.0880 172.7180 x,y,z range (A): 50.72300 59.69201 66.63000 scale (grids/A): 2.404322 object centre (A): 14.20650 97.18900 139.4030 number of atom coordinates read : 3166 total number of charged atoms : 3027 net assigned charge : -5.999976 assigned positive charge : 471.9338 centred at (gu) : 84.61091 96.70746 103.6551 assigned negative charge : -477.9349 centred at (gu) : 84.80946 96.67067 103.7748 start vw surface at 0.1600000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 147061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27401 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 66711 mr = 104729 m= 18276 mr = 52764 m= 2784 mr = 13837 m= 165 mr = 1791 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 831 time to turn everything in is 1.090000 number of dielectric boundary points 61825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 24170 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) : 1.602881 object centre at (A) : 14.20650 97.18900 139.4030 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4220403 -0.3369339 midg,1,midg; midg,igrid,midg 3.2011321E-04 0.1717724 1,midg,midg; igrid,midg,midg -3.5513636E-02 -8.1740797E-02 gauss-seidel spectral radius is 0.9991170 estimated iterations to convergence 266 setup time was (sec) 1.390000 now iterating at: 03:14:40 rms-change max change #iterations 8.611889 283.2614 at 10iterations 4.808957 123.5358 at 20iterations 2.660593 64.20970 at 30iterations 1.471251 37.90386 at 40iterations 0.8096626 18.08326 at 50iterations 0.4449935 10.08098 at 60iterations 0.2441370 6.325764 at 70iterations 0.1334412 2.731602 at 80iterations 7.3037878E-02 1.807613 at 90iterations 3.9856743E-02 0.8154784 at 100iterations 2.1747246E-02 0.4204187 at 110iterations 1.1875380E-02 0.2427464 at 120iterations 6.4765019E-03 0.1514549 at 130iterations 3.5473800E-03 7.5199127E-02 at 140iterations 1.9336087E-03 3.7147522E-02 at 150iterations 1.0557079E-03 2.3533344E-02 at 160iterations 5.7888811E-04 1.1621952E-02 at 170iterations 3.1786400E-04 6.9580078E-03 at 180iterations finished qdiffx linear iterations at : 03:14:50 total time elapsed so far: 11.51000 # loops : 180 mean,max change (kT/e) : 3.1786400E-04 6.9580078E-03 energy calculations done at 11.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.68000 DelPhi exited at 03:14:50 11.678u 0.232s 0:12.30 96.7% 0+0k 0+0io 0pf+0w