Sun Oct 9 13:27:12 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+sph2.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 = amb2.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 13:27:12 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2405 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7100687 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): 30.34600 78.41900 ymin,ymax (A): 16.45600 66.59200 zmin,zma (A): 3.228000 46.89000 x,y,z range (A): 48.07300 50.13599 43.66200 scale (grids/A): 0.7100687 object centre (A): 54.38250 41.52400 25.05900 number of atom coordinates read : 2405 total number of charged atoms : 2262 net assigned charge : 3.500028 assigned positive charge : 371.7850 centred at (gu) : 90.74369 90.96809 90.36370 assigned negative charge : -368.2855 centred at (gu) : 90.89106 91.12424 90.49727 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8146 nv = 96 ne = 84 npr = 48257 no. pairs analyzed = 48257 no. exposed pairs = 3081 no. arc points = 20835 no. surface atoms = 1045 nbur = 1360 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 552 mr = 4561 m= 2 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1949 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9165 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0724500E-07 -5.3762843E-08 midg,1,midg; midg,igrid,midg 1.0656305E-07 -7.8418594E-08 1,midg,midg; igrid,midg,midg 1.0676228E-07 -6.8365210E-08 gauss-seidel spectral radius is 0.9896944 estimated iterations to convergence 80 setup time was (sec) 0.4000000 now iterating at: 13:27:12 rms-change max change #iterations 0.2252306 29.91819 at 10iterations 2.8989315E-02 3.723110 at 20iterations 4.1895802E-03 0.5577316 at 30iterations 9.7407936E-04 0.1366272 at 40iterations 3.1930802E-04 4.5303345E-02 at 50iterations finished qdiffx linear iterations at : 13:27:15 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 3.1930802E-04 4.5303345E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 13:27:15 3.392u 0.152s 0:03.81 92.9% 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 13:27:15 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2405 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.130206 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): 30.34600 78.41900 ymin,ymax (A): 16.45600 66.59200 zmin,zma (A): 3.228000 46.89000 x,y,z range (A): 48.07300 50.13599 43.66200 scale (grids/A): 2.130206 object centre (A): 54.38250 41.52400 25.05900 number of atom coordinates read : 2405 total number of charged atoms : 2262 net assigned charge : 3.500028 assigned positive charge : 371.7850 centred at (gu) : 92.23044 92.90384 91.09042 assigned negative charge : -368.2855 centred at (gu) : 92.67286 93.37242 91.49149 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 86057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20835 grid for indexing accessible points = 1.400000 m= 34494 mr = 60077 m= 7121 mr = 26061 m= 709 mr = 4853 m= 19 mr = 308 m= 0 mr = 1 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 37100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 17967 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) : 0.7100687 object centre at (A) : 54.38250 41.52400 25.05900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4641924E-02 1.1455309E-02 midg,1,midg; midg,igrid,midg 5.7099396E-03 -8.9392826E-02 1,midg,midg; igrid,midg,midg -5.3798612E-03 -2.4781812E-02 gauss-seidel spectral radius is 0.9988751 estimated iterations to convergence 236 setup time was (sec) 0.6500000 now iterating at: 13:27:16 rms-change max change #iterations 5.158470 219.0333 at 10iterations 2.577069 80.66430 at 20iterations 1.294048 37.64891 at 30iterations 0.6524813 20.84868 at 40iterations 0.3274113 8.848751 at 50iterations 0.1648476 4.820923 at 60iterations 8.3079949E-02 2.501672 at 70iterations 4.1775256E-02 1.123035 at 80iterations 2.1274580E-02 0.5715251 at 90iterations 1.0969141E-02 0.3146515 at 100iterations 5.7083284E-03 0.1701508 at 110iterations 3.0969258E-03 9.3154907E-02 at 120iterations finished qdiffx linear iterations at : 13:27:23 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 3.0969258E-03 9.3154907E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 13:27:24 7.895u 0.197s 0:08.36 96.6% 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 13:27:24 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2405 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.195309 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): 30.34600 78.41900 ymin,ymax (A): 16.45600 66.59200 zmin,zma (A): 3.228000 46.89000 x,y,z range (A): 48.07300 50.13599 43.66200 scale (grids/A): 3.195309 object centre (A): 54.38250 41.52400 25.05900 number of atom coordinates read : 2405 total number of charged atoms : 2262 net assigned charge : 3.500028 assigned positive charge : 371.7850 centred at (gu) : 93.34566 94.35566 91.63557 assigned negative charge : -368.2855 centred at (gu) : 94.00930 95.05859 92.23715 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 198337 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20835 grid for indexing accessible points = 1.400000 m= 106382 mr = 145011 m= 44553 mr = 87780 m= 13556 mr = 36772 m= 2764 mr = 10517 m= 268 mr = 2004 m= 11 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 83664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 18096 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) : 2.130206 object centre at (A) : 54.38250 41.52400 25.05900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7897758 -9.1842907E-03 midg,1,midg; midg,igrid,midg -0.3460759 -0.7221488 1,midg,midg; igrid,midg,midg -0.1587992 -0.3966362 gauss-seidel spectral radius is 0.9993134 estimated iterations to convergence 301 setup time was (sec) 1.580000 now iterating at: 13:27:26 rms-change max change #iterations 11.49486 486.2402 at 10iterations 6.879073 127.4861 at 20iterations 4.100862 75.00451 at 30iterations 2.444225 41.81666 at 40iterations 1.449213 23.86137 at 50iterations 0.8606377 13.85239 at 60iterations 0.5093969 8.460094 at 70iterations 0.3004933 4.815452 at 80iterations 0.1773962 2.769089 at 90iterations 0.1050488 1.784531 at 100iterations 6.2072221E-02 1.090719 at 110iterations 3.6840349E-02 0.6195937 at 120iterations 2.2010198E-02 0.3798141 at 130iterations 1.3341880E-02 0.2510071 at 140iterations 8.3187046E-03 0.1711082 at 150iterations 5.3927968E-03 0.1082859 at 160iterations 3.6981076E-03 7.3390961E-02 at 170iterations 2.7107904E-03 6.1592102E-02 at 180iterations finished qdiffx linear iterations at : 13:27:37 total time elapsed so far: 13.05000 # loops : 180 mean,max change (kT/e) : 2.7107904E-03 6.1592102E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 13:27:38 13.178u 0.221s 0:13.66 98.0% 0+0k 0+0io 0pf+0w