Tue Oct 11 03:19:42 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 Tue Oct 11 2011 at 03:19:42 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 !!! WARNING: GLM 16 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5376425 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): -42.98900 10.77800 ymin,ymax (A): -55.92000 3.374000 zmin,zma (A): -34.45400 31.76100 x,y,z range (A): 53.76700 59.29400 66.21500 scale (grids/A): 0.5376425 object centre (A): -16.10550 -26.27300 -1.346501 number of atom coordinates read : 3415 total number of charged atoms : 3270 net assigned charge : -6.093972 assigned positive charge : 518.9723 centred at (gu) : 91.44710 87.92810 92.24433 assigned negative charge : -525.0678 centred at (gu) : 91.41423 87.89716 92.24751 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6422 nv = 96 ne = 84 npr = 69194 no. pairs analyzed = 69194 no. exposed pairs = 4286 no. arc points = 30340 no. surface atoms = 1434 nbur = 1981 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 = 1.596000 m= 260 mr = 3328 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3148 ## 469 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8491 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4549732E-10 -4.9642712E-10 midg,1,midg; midg,igrid,midg -7.4369527E-10 -5.9230315E-11 1,midg,midg; igrid,midg,midg -3.1712102E-10 -1.1328699E-10 gauss-seidel spectral radius is 0.9822024 estimated iterations to convergence 62 setup time was (sec) 0.7300000 now iterating at: 03:19:44 rms-change max change #iterations 7.5946271E-02 13.80099 at 10iterations 5.1360317E-03 0.7961254 at 20iterations 5.8783882E-04 8.4070206E-02 at 30iterations 1.3741586E-04 1.7625809E-02 at 40iterations 3.7400565E-05 4.7206879E-03 at 50iterations finished qdiffx linear iterations at : 03:19:48 total time elapsed so far: 5.670000 # loops : 50 mean,max change (kT/e) : 3.7400565E-05 4.7206879E-03 energy calculations done at 5.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.840000 DelPhi exited at 03:19:49 5.848u 0.418s 0:06.66 93.8% 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 Tue Oct 11 2011 at 03:19:49 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 !!! WARNING: GLM 16 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.612927 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): -42.98900 10.77800 ymin,ymax (A): -55.92000 3.374000 zmin,zma (A): -34.45400 31.76100 x,y,z range (A): 53.76700 59.29400 66.21500 scale (grids/A): 1.612927 object centre (A): -16.10550 -26.27300 -1.346501 number of atom coordinates read : 3415 total number of charged atoms : 3270 net assigned charge : -6.093972 assigned positive charge : 518.9723 centred at (gu) : 94.34040 83.78342 96.73206 assigned negative charge : -525.0678 centred at (gu) : 94.24222 83.69099 96.74235 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71336 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30340 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21841 mr = 48506 m= 2247 mr = 14803 m= 65 mr = 1026 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 394 time to turn everything in is 0.6200000 number of dielectric boundary points 31149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 405 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 24931 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) : 0.5376425 object centre at (A) : -16.10550 -26.27300 -1.346501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4317790E-02 -1.4236603E-02 midg,1,midg; midg,igrid,midg -5.8565261E-03 -9.2507160E-04 1,midg,midg; igrid,midg,midg -6.1552911E-03 -2.2354578E-03 gauss-seidel spectral radius is 0.9981767 estimated iterations to convergence 186 setup time was (sec) 0.9700000 now iterating at: 03:19:51 rms-change max change #iterations 3.557364 181.0160 at 10iterations 1.471995 54.54589 at 20iterations 0.6133568 25.97809 at 30iterations 0.2554574 8.732632 at 40iterations 0.1066965 4.045877 at 50iterations 4.4238739E-02 1.549464 at 60iterations 1.8486340E-02 0.6940327 at 70iterations 7.7916146E-03 0.2853584 at 80iterations 3.3301644E-03 0.1224365 at 90iterations 1.4659130E-03 4.9182415E-02 at 100iterations 6.7925785E-04 2.5453568E-02 at 110iterations 3.4455568E-04 1.1786938E-02 at 120iterations finished qdiffx linear iterations at : 03:20:03 total time elapsed so far: 13.70000 # loops : 120 mean,max change (kT/e) : 3.4455568E-04 1.1786938E-02 energy calculations done at 13.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.87000 DelPhi exited at 03:20:04 13.878u 0.490s 0:14.87 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 Tue Oct 11 2011 at 03:20:04 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 !!! WARNING: GLM 16 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.419391 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): -42.98900 10.77800 ymin,ymax (A): -55.92000 3.374000 zmin,zma (A): -34.45400 31.76100 x,y,z range (A): 53.76700 59.29400 66.21500 scale (grids/A): 2.419391 object centre (A): -16.10550 -26.27300 -1.346501 number of atom coordinates read : 3415 total number of charged atoms : 3270 net assigned charge : -6.093972 assigned positive charge : 518.9723 centred at (gu) : 96.51039 80.67485 100.0979 assigned negative charge : -525.0678 centred at (gu) : 96.36320 80.53641 100.1134 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 166027 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30340 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 76309 mr = 119093 m= 21119 mr = 59912 m= 3467 mr = 15588 m= 224 mr = 2174 m= 3 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 1295 time to turn everything in is 1.500000 number of dielectric boundary points 70303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 26123 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) : 1.612927 object centre at (A) : -16.10550 -26.27300 -1.346501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4420249 -0.3635560 midg,1,midg; midg,igrid,midg -3.4769140E-02 3.4157779E-02 1,midg,midg; igrid,midg,midg -0.1010005 -2.7703691E-02 gauss-seidel spectral radius is 0.9991438 estimated iterations to convergence 270 setup time was (sec) 1.900000 now iterating at: 03:20:06 rms-change max change #iterations 9.293259 309.8064 at 10iterations 5.255847 132.7825 at 20iterations 2.951110 63.51591 at 30iterations 1.648541 35.87527 at 40iterations 0.9172406 20.01315 at 50iterations 0.5107482 10.94568 at 60iterations 0.2832288 5.933437 at 70iterations 0.1567489 3.367982 at 80iterations 8.6943693E-02 1.931385 at 90iterations 4.8043203E-02 0.9946079 at 100iterations 2.6483919E-02 0.5092473 at 110iterations 1.4670669E-02 0.2910981 at 120iterations 8.1156250E-03 0.1671295 at 130iterations 4.5057433E-03 9.0759277E-02 at 140iterations 2.5042805E-03 4.8142433E-02 at 150iterations 1.4018994E-03 2.8897285E-02 at 160iterations 7.9313770E-04 1.5449524E-02 at 170iterations 4.5845509E-04 9.7938776E-03 at 180iterations finished qdiffx linear iterations at : 03:20:27 total time elapsed so far: 22.37000 # loops : 180 mean,max change (kT/e) : 4.5845509E-04 9.7938776E-03 energy calculations done at 22.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.53000 DelPhi exited at 03:20:28 22.536u 0.507s 0:23.75 96.9% 0+0k 0+0io 0pf+0w