Sat Oct 8 18:25:17 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 8 2011 at 18:25:17 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 = 3377 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5726879 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): -27.00100 24.75300 ymin,ymax (A): 18.23500 80.39800 zmin,zma (A): -11.99500 43.07700 x,y,z range (A): 51.75400 62.16300 55.07200 scale (grids/A): 0.5726879 object centre (A): -1.124000 49.31650 15.54100 number of atom coordinates read : 3377 total number of charged atoms : 3232 net assigned charge : 8.500029 assigned positive charge : 513.6724 centred at (gu) : 91.24746 88.73347 89.00475 assigned negative charge : -505.1739 centred at (gu) : 91.23346 88.79321 88.94244 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7477 nv = 96 ne = 84 npr = 65615 no. pairs analyzed = 65615 no. exposed pairs = 4711 no. arc points = 33834 no. surface atoms = 1539 nbur = 1838 mkacc time = 0.1100000 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 = 1.512000 m= 373 mr = 3704 m= 3 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2500000 number of dielectric boundary points 4122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3351 ## 419 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9490 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3273186E-10 2.0831357E-09 midg,1,midg; midg,igrid,midg 3.4786958E-09 2.0073106E-10 1,midg,midg; igrid,midg,midg 8.6832586E-10 2.2669198E-09 gauss-seidel spectral radius is 0.9843102 estimated iterations to convergence 66 setup time was (sec) 0.4400000 now iterating at: 18:25:17 rms-change max change #iterations 9.9571653E-02 14.31620 at 10iterations 8.8760545E-03 1.412956 at 20iterations 1.8685275E-03 0.3550797 at 30iterations 6.8578293E-04 0.1312943 at 40iterations 2.6320090E-04 5.0426483E-02 at 50iterations finished qdiffx linear iterations at : 18:25:20 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.6320090E-04 5.0426483E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 18:25:21 3.415u 0.157s 0:03.86 92.2% 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 Sat Oct 8 2011 at 18:25:21 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 = 3377 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.718064 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): -27.00100 24.75300 ymin,ymax (A): 18.23500 80.39800 zmin,zma (A): -11.99500 43.07700 x,y,z range (A): 51.75400 62.16300 55.07200 scale (grids/A): 1.718064 object centre (A): -1.124000 49.31650 15.54100 number of atom coordinates read : 3377 total number of charged atoms : 3232 net assigned charge : 8.500029 assigned positive charge : 513.6724 centred at (gu) : 93.74139 86.19968 87.01324 assigned negative charge : -505.1739 centred at (gu) : 93.70007 86.37922 86.82693 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33834 grid for indexing accessible points = 1.400000 m= 27840 mr = 53140 m= 3804 mr = 19106 m= 144 mr = 2006 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 927 time to turn everything in is 0.3900000 number of dielectric boundary points 38519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 338 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 25036 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) : 0.5726879 object centre at (A) : -1.124000 49.31650 15.54100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3724639E-03 9.8505449E-03 midg,1,midg; midg,igrid,midg 3.3276018E-02 4.1939318E-03 1,midg,midg; igrid,midg,midg 5.0515593E-03 1.3887072E-02 gauss-seidel spectral radius is 0.9984206 estimated iterations to convergence 200 setup time was (sec) 0.6100000 now iterating at: 18:25:21 rms-change max change #iterations 3.975698 161.9210 at 10iterations 1.743679 75.29929 at 20iterations 0.7705801 24.89423 at 30iterations 0.3413382 11.59624 at 40iterations 0.1505615 4.956306 at 50iterations 6.6846848E-02 2.207796 at 60iterations 2.9846961E-02 1.012909 at 70iterations 1.3599475E-02 0.4623489 at 80iterations 6.4824745E-03 0.2459106 at 90iterations 3.3616044E-03 0.1383820 at 100iterations 1.9324612E-03 7.4069977E-02 at 110iterations 1.2390311E-03 4.8355103E-02 at 120iterations finished qdiffx linear iterations at : 18:25:28 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 1.2390311E-03 4.8355103E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 18:25:29 7.824u 0.199s 0:08.29 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 Sat Oct 8 2011 at 18:25:29 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 = 3377 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.577096 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): -27.00100 24.75300 ymin,ymax (A): 18.23500 80.39800 zmin,zma (A): -11.99500 43.07700 x,y,z range (A): 51.75400 62.16300 55.07200 scale (grids/A): 2.577096 object centre (A): -1.124000 49.31650 15.54100 number of atom coordinates read : 3377 total number of charged atoms : 3232 net assigned charge : 8.500029 assigned positive charge : 513.6724 centred at (gu) : 95.61184 84.29921 85.51972 assigned negative charge : -505.1739 centred at (gu) : 95.54986 84.56866 85.24030 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 187480 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33834 grid for indexing accessible points = 1.400000 m= 91246 mr = 130389 m= 30984 mr = 71240 m= 6274 mr = 23534 m= 545 mr = 4089 m= 26 mr = 237 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 2899 time to turn everything in is 1.000000 number of dielectric boundary points 87061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 25844 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) : 1.718064 object centre at (A) : -1.124000 49.31650 15.54100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4323575E-02 0.1178010 midg,1,midg; midg,igrid,midg 0.3728368 3.9426122E-02 1,midg,midg; igrid,midg,midg 5.3890564E-02 0.1796596 gauss-seidel spectral radius is 0.9992249 estimated iterations to convergence 284 setup time was (sec) 1.240000 now iterating at: 18:25:30 rms-change max change #iterations 10.19617 346.5356 at 10iterations 6.000569 152.5240 at 20iterations 3.493831 84.82839 at 30iterations 2.021774 44.06199 at 40iterations 1.167935 26.74937 at 50iterations 0.6710323 14.59125 at 60iterations 0.3840202 7.125729 at 70iterations 0.2193491 4.802135 at 80iterations 0.1255170 2.904907 at 90iterations 7.1540251E-02 1.384186 at 100iterations 4.0694203E-02 0.7458916 at 110iterations 2.3247646E-02 0.4887428 at 120iterations 1.3273073E-02 0.2670317 at 130iterations 7.6051052E-03 0.1764984 at 140iterations 4.3891459E-03 8.5098267E-02 at 150iterations 2.5742888E-03 4.9831390E-02 at 160iterations 1.5501227E-03 3.2997131E-02 at 170iterations 9.7572600E-04 2.2388458E-02 at 180iterations finished qdiffx linear iterations at : 18:25:42 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 9.7572600E-04 2.2388458E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 18:25:42 12.752u 0.202s 0:13.29 97.4% 0+0k 0+0io 0pf+0w