Sat Oct 15 13:11:01 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 Sat Oct 15 2011 at 13:11:01 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5431 !!! WARNING: HIR 862 has a net charge of 0.5140 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: 0.5111784 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): -16.61200 53.03100 ymin,ymax (A): 98.59500 167.3340 zmin,zma (A): -29.84200 31.71300 x,y,z range (A): 69.64301 68.73900 61.55500 scale (grids/A): 0.5111784 object centre (A): 18.20950 132.9645 0.9355001 number of atom coordinates read : 5431 total number of charged atoms : 5259 net assigned charge : -5.985967 assigned positive charge : 831.9492 centred at (gu) : 89.59586 88.72189 88.01005 assigned negative charge : -837.9418 centred at (gu) : 89.58636 88.81011 87.96465 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8717 nv = 96 ne = 84 npr = 111550 no. pairs analyzed = 111550 no. exposed pairs = 6305 no. arc points = 43677 no. surface atoms = 2130 nbur = 3301 mkacc time = 0.1900000 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 = 1.680000 m= 288 mr = 4777 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3600000 number of dielectric boundary points 4226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4206 ## 582 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 11800 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8821230E-10 2.9951968E-11 midg,1,midg; midg,igrid,midg 2.5985508E-10 -2.5989189E-10 1,midg,midg; igrid,midg,midg -1.2941069E-10 -5.2221595E-11 gauss-seidel spectral radius is 0.9804619 estimated iterations to convergence 59 setup time was (sec) 0.5500000 now iterating at: 13:11:02 rms-change max change #iterations 7.3317282E-02 9.300117 at 10iterations 5.0359154E-03 0.7950897 at 20iterations 7.2326331E-04 0.1095200 at 30iterations 1.6560382E-04 2.3242950E-02 at 40iterations 4.0404266E-05 5.4664612E-03 at 50iterations finished qdiffx linear iterations at : 13:11:05 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 4.0404266E-05 5.4664612E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 13:11:05 3.626u 0.198s 0:04.09 93.1% 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 15 2011 at 13:11:05 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5431 !!! WARNING: HIR 862 has a net charge of 0.5140 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: 1.533535 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): -16.61200 53.03100 ymin,ymax (A): 98.59500 167.3340 zmin,zma (A): -29.84200 31.71300 x,y,z range (A): 69.64301 68.73900 61.55500 scale (grids/A): 1.533535 object centre (A): 18.20950 132.9645 0.9355001 number of atom coordinates read : 5431 total number of charged atoms : 5259 net assigned charge : -5.985967 assigned positive charge : 831.9492 centred at (gu) : 88.78616 86.16391 84.02894 assigned negative charge : -837.9418 centred at (gu) : 88.75859 86.43003 83.89369 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 99559 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43677 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 29440 mr = 70653 m= 2546 mr = 20288 m= 49 mr = 1122 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2537 time to turn everything in is 0.4700000 number of dielectric boundary points 39531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 540 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 39397 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) : 0.5111784 object centre at (A) : 18.20950 132.9645 0.9355001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1572390E-04 -6.1271773E-03 midg,1,midg; midg,igrid,midg 2.1595217E-02 -1.4874619E-02 1,midg,midg; igrid,midg,midg -2.6252924E-02 -7.2448310E-03 gauss-seidel spectral radius is 0.9981514 estimated iterations to convergence 185 setup time was (sec) 0.7000000 now iterating at: 13:11:06 rms-change max change #iterations 4.148859 167.0037 at 10iterations 1.717449 52.99245 at 20iterations 0.7135507 22.37934 at 30iterations 0.2967262 8.792633 at 40iterations 0.1227465 3.441910 at 50iterations 5.1044226E-02 1.519807 at 60iterations 2.1292936E-02 0.6401615 at 70iterations 8.8566318E-03 0.3052330 at 80iterations 3.7095621E-03 0.1099701 at 90iterations 1.5754265E-03 4.8821211E-02 at 100iterations 6.7761284E-04 2.3643494E-02 at 110iterations 2.9776600E-04 9.5100403E-03 at 120iterations finished qdiffx linear iterations at : 13:11:13 total time elapsed so far: 8.020000 # loops : 120 mean,max change (kT/e) : 2.9776600E-04 9.5100403E-03 energy calculations done at 8.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 13:11:14 8.162u 0.226s 0:08.76 95.6% 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 15 2011 at 13:11:14 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5431 !!! WARNING: HIR 862 has a net charge of 0.5140 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: 2.300303 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): -16.61200 53.03100 ymin,ymax (A): 98.59500 167.3340 zmin,zma (A): -29.84200 31.71300 x,y,z range (A): 69.64301 68.73900 61.55500 scale (grids/A): 2.300303 object centre (A): 18.20950 132.9645 0.9355001 number of atom coordinates read : 5431 total number of charged atoms : 5259 net assigned charge : -5.985967 assigned positive charge : 831.9492 centred at (gu) : 88.17888 84.24538 81.04305 assigned negative charge : -837.9418 centred at (gu) : 88.13782 84.64494 80.84051 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 232778 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43677 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 105230 mr = 173573 m= 27297 mr = 83615 m= 3712 mr = 20397 m= 180 mr = 2290 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 8364 time to turn everything in is 1.180000 number of dielectric boundary points 89290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 41979 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) : 1.533535 object centre at (A) : 18.20950 132.9645 0.9355001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1200297 -0.1444720 midg,1,midg; midg,igrid,midg 0.4065219 -0.2169716 1,midg,midg; igrid,midg,midg -0.2818465 -8.7235935E-02 gauss-seidel spectral radius is 0.9991744 estimated iterations to convergence 275 setup time was (sec) 1.440000 now iterating at: 13:11:15 rms-change max change #iterations 11.11602 283.5146 at 10iterations 6.349946 179.5604 at 20iterations 3.603800 81.96813 at 30iterations 2.030376 41.20386 at 40iterations 1.141048 22.34324 at 50iterations 0.6412127 11.86177 at 60iterations 0.3593483 6.783232 at 70iterations 0.2012702 3.601555 at 80iterations 0.1122629 1.940491 at 90iterations 6.2620692E-02 1.057251 at 100iterations 3.4986727E-02 0.5734644 at 110iterations 1.9504683E-02 0.3308792 at 120iterations 1.0897941E-02 0.1844909 at 130iterations 6.0858158E-03 0.1162891 at 140iterations 3.3986617E-03 5.7525635E-02 at 150iterations 1.8971345E-03 3.4725189E-02 at 160iterations 1.0613432E-03 1.7620087E-02 at 170iterations 5.9300452E-04 1.0408401E-02 at 180iterations finished qdiffx linear iterations at : 13:11:27 total time elapsed so far: 13.38000 # loops : 180 mean,max change (kT/e) : 5.9300452E-04 1.0408401E-02 energy calculations done at 13.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.51000 DelPhi exited at 13:11:28 13.514u 0.226s 0:14.02 97.9% 0+0k 0+0io 0pf+0w