Sat Oct 8 12:34:59 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 12:34:59 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 = 2313 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: 0.6114002 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): -17.96100 21.39000 ymin,ymax (A): -17.93400 31.87200 zmin,zma (A): 18.52200 76.74900 x,y,z range (A): 39.35100 49.80600 58.22700 scale (grids/A): 0.6114002 object centre (A): 1.714499 6.969000 47.63550 number of atom coordinates read : 2313 total number of charged atoms : 2179 net assigned charge : 2.000007 assigned positive charge : 310.9947 centred at (gu) : 90.35986 89.49737 88.76917 assigned negative charge : -308.9954 centred at (gu) : 90.30704 89.57297 89.00341 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5876 nv = 96 ne = 84 npr = 49620 no. pairs analyzed = 49620 no. exposed pairs = 3076 no. arc points = 21139 no. surface atoms = 1055 nbur = 1258 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 297 mr = 2956 m= 0 mr = 17 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3200 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2032 ## 147 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7128 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3829969E-08 -6.6426198E-09 midg,1,midg; midg,igrid,midg 4.6614637E-09 -1.8174063E-09 1,midg,midg; igrid,midg,midg -1.0041301E-09 3.5132328E-09 gauss-seidel spectral radius is 0.9861341 estimated iterations to convergence 70 setup time was (sec) 0.5800000 now iterating at: 12:35:00 rms-change max change #iterations 0.1044446 17.84585 at 10iterations 1.0148183E-02 1.590324 at 20iterations 2.1421206E-03 0.4188232 at 30iterations 8.8174094E-04 0.1791878 at 40iterations 3.8862778E-04 7.9074860E-02 at 50iterations finished qdiffx linear iterations at : 12:35:03 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 3.8862778E-04 7.9074860E-02 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 12:35:03 4.126u 0.292s 0:04.72 93.4% 0+0k 0+0io 5pf+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 12:35:03 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 = 2313 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: 1.834201 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): -17.96100 21.39000 ymin,ymax (A): -17.93400 31.87200 zmin,zma (A): 18.52200 76.74900 x,y,z range (A): 39.35100 49.80600 58.22700 scale (grids/A): 1.834201 object centre (A): 1.714499 6.969000 47.63550 number of atom coordinates read : 2313 total number of charged atoms : 2179 net assigned charge : 2.000007 assigned positive charge : 310.9947 centred at (gu) : 91.07941 88.49180 86.30740 assigned negative charge : -308.9954 centred at (gu) : 90.92116 88.71895 87.01025 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 63251 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21139 grid for indexing accessible points = 1.400000 m= 20615 mr = 41802 m= 3054 mr = 13860 m= 136 mr = 1698 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 29669 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 17093 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) : 0.6114002 object centre at (A) : 1.714499 6.969000 47.63550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6449166E-02 -2.1515228E-02 midg,1,midg; midg,igrid,midg 4.2314939E-03 1.0063841E-05 1,midg,midg; igrid,midg,midg 3.3742221E-04 5.7162819E-03 gauss-seidel spectral radius is 0.9985079 estimated iterations to convergence 205 setup time was (sec) 0.8600000 now iterating at: 12:35:05 rms-change max change #iterations 3.463426 152.0263 at 10iterations 1.555546 57.60165 at 20iterations 0.7053400 24.23759 at 30iterations 0.3187694 11.15072 at 40iterations 0.1445798 5.322548 at 50iterations 6.5582484E-02 2.409111 at 60iterations 3.0052803E-02 1.129215 at 70iterations 1.3924342E-02 0.4987297 at 80iterations 6.6792099E-03 0.2600403 at 90iterations 3.4794477E-03 0.1425896 at 100iterations 2.0351601E-03 9.0736389E-02 at 110iterations 1.3499984E-03 5.6644440E-02 at 120iterations finished qdiffx linear iterations at : 12:35:13 total time elapsed so far: 9.320000 # loops : 120 mean,max change (kT/e) : 1.3499984E-03 5.6644440E-02 energy calculations done at 9.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.500000 DelPhi exited at 12:35:14 9.499u 0.334s 0:10.18 96.4% 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 12:35:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2313 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: 2.751301 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): -17.96100 21.39000 ymin,ymax (A): -17.93400 31.87200 zmin,zma (A): 18.52200 76.74900 x,y,z range (A): 39.35100 49.80600 58.22700 scale (grids/A): 2.751301 object centre (A): 1.714499 6.969000 47.63550 number of atom coordinates read : 2313 total number of charged atoms : 2179 net assigned charge : 2.000007 assigned positive charge : 310.9947 centred at (gu) : 91.61916 87.73764 84.46101 assigned negative charge : -308.9954 centred at (gu) : 91.38173 88.07845 85.51537 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 146643 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21139 grid for indexing accessible points = 1.400000 m= 67766 mr = 102413 m= 23230 mr = 52700 m= 5289 mr = 17503 m= 632 mr = 3728 m= 19 mr = 354 m= 0 mr = 5 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.450000 number of dielectric boundary points 66876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 17430 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) : 1.834201 object centre at (A) : 1.714499 6.969000 47.63550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6017172 -0.1797318 midg,1,midg; midg,igrid,midg 2.9969871E-02 -9.1519449E-03 1,midg,midg; igrid,midg,midg -8.5162530E-03 4.2658586E-02 gauss-seidel spectral radius is 0.9992239 estimated iterations to convergence 283 setup time was (sec) 1.780000 now iterating at: 12:35:16 rms-change max change #iterations 8.337965 267.0303 at 10iterations 4.836898 150.3042 at 20iterations 2.778888 63.64244 at 30iterations 1.597003 34.88492 at 40iterations 0.9142249 20.05186 at 50iterations 0.5212130 10.90969 at 60iterations 0.2975059 6.696869 at 70iterations 0.1699581 3.745346 at 80iterations 9.6574448E-02 1.966583 at 90iterations 5.5214621E-02 1.095818 at 100iterations 3.1399932E-02 0.6217308 at 110iterations 1.7956683E-02 0.4320984 at 120iterations 1.0292036E-02 0.2372818 at 130iterations 5.9752092E-03 0.1234131 at 140iterations 3.5576483E-03 8.3278656E-02 at 150iterations 2.2089009E-03 5.4092407E-02 at 160iterations 1.4676207E-03 3.6285400E-02 at 170iterations 1.0560134E-03 2.6679993E-02 at 180iterations finished qdiffx linear iterations at : 12:35:30 total time elapsed so far: 15.79000 # loops : 180 mean,max change (kT/e) : 1.0560134E-03 2.6679993E-02 energy calculations done at 15.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.98000 DelPhi exited at 12:35:30 15.984u 0.320s 0:16.60 98.1% 0+0k 0+0io 0pf+0w