Mon Oct 10 23:15:12 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 Mon Oct 10 2011 at 23:15:12 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2562 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: 0.5790595 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): -11.03700 50.44200 ymin,ymax (A): -7.126000 43.22400 zmin,zma (A): -7.543000 33.15700 x,y,z range (A): 61.47900 50.35000 40.70000 scale (grids/A): 0.5790595 object centre (A): 19.70250 18.04900 12.80700 number of atom coordinates read : 2562 total number of charged atoms : 2426 net assigned charge : 8.500022 assigned positive charge : 385.9568 centred at (gu) : 92.82192 90.42687 90.13171 assigned negative charge : -377.4576 centred at (gu) : 92.69164 90.35597 90.21148 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5364 nv = 96 ne = 84 npr = 53272 no. pairs analyzed = 53272 no. exposed pairs = 2981 no. arc points = 21168 no. surface atoms = 997 nbur = 1565 mkacc time = 0.1400000 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 = 1.484000 m= 228 mr = 2908 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.2900000 number of dielectric boundary points 2674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2048 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6960 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0297134E-09 2.6404526E-10 midg,1,midg; midg,igrid,midg 3.8820605E-10 3.2764893E-09 1,midg,midg; igrid,midg,midg -3.1556166E-10 7.8357605E-09 gauss-seidel spectral radius is 0.9845634 estimated iterations to convergence 66 setup time was (sec) 0.6100000 now iterating at: 23:15:13 rms-change max change #iterations 9.3090944E-02 15.94737 at 10iterations 7.9883151E-03 1.698196 at 20iterations 1.0739125E-03 0.2742233 at 30iterations 2.5446291E-04 7.0446014E-02 at 40iterations 6.5591070E-05 1.8741608E-02 at 50iterations finished qdiffx linear iterations at : 23:15:18 total time elapsed so far: 4.840000 # loops : 50 mean,max change (kT/e) : 6.5591070E-05 1.8741608E-02 energy calculations done at 4.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.010000 DelPhi exited at 23:15:18 5.012u 0.444s 0:05.93 91.9% 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 Mon Oct 10 2011 at 23:15:18 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2562 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: 1.737179 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): -11.03700 50.44200 ymin,ymax (A): -7.126000 43.22400 zmin,zma (A): -7.543000 33.15700 x,y,z range (A): 61.47900 50.35000 40.70000 scale (grids/A): 1.737179 object centre (A): 19.70250 18.04900 12.80700 number of atom coordinates read : 2562 total number of charged atoms : 2426 net assigned charge : 8.500022 assigned positive charge : 385.9568 centred at (gu) : 98.46542 91.28012 90.39462 assigned negative charge : -377.4576 centred at (gu) : 98.07458 91.06783 90.63421 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59513 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21168 grid for indexing accessible points = 1.400000 m= 18004 mr = 41097 m= 1970 mr = 12649 m= 57 mr = 1051 m= 0 mr = 5 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1861 time to turn everything in is 0.4700000 number of dielectric boundary points 24742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 18855 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) : 0.5790595 object centre at (A) : 19.70250 18.04900 12.80700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5556419E-02 6.5636118E-03 midg,1,midg; midg,igrid,midg 1.1635270E-02 1.8591009E-02 1,midg,midg; igrid,midg,midg 2.3223967E-03 -2.0544787E-03 gauss-seidel spectral radius is 0.9983441 estimated iterations to convergence 195 setup time was (sec) 0.8400000 now iterating at: 23:15:20 rms-change max change #iterations 3.446913 186.8515 at 10iterations 1.490255 65.85189 at 20iterations 0.6469079 24.62292 at 30iterations 0.2807131 10.67945 at 40iterations 0.1223244 4.607754 at 50iterations 5.3150289E-02 2.185429 at 60iterations 2.3199404E-02 0.7932129 at 70iterations 1.0171846E-02 0.3718719 at 80iterations 4.5629260E-03 0.1698118 at 90iterations 2.0895984E-03 8.4514618E-02 at 100iterations 1.0090623E-03 4.0218353E-02 at 110iterations 5.1038561E-04 2.4780273E-02 at 120iterations finished qdiffx linear iterations at : 23:15:31 total time elapsed so far: 11.76000 # loops : 120 mean,max change (kT/e) : 5.1038561E-04 2.4780273E-02 energy calculations done at 11.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.92000 DelPhi exited at 23:15:31 11.927u 0.510s 0:12.87 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 Mon Oct 10 2011 at 23:15:31 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2562 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: 2.605768 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): -11.03700 50.44200 ymin,ymax (A): -7.126000 43.22400 zmin,zma (A): -7.543000 33.15700 x,y,z range (A): 61.47900 50.35000 40.70000 scale (grids/A): 2.605768 object centre (A): 19.70250 18.04900 12.80700 number of atom coordinates read : 2562 total number of charged atoms : 2426 net assigned charge : 8.500022 assigned positive charge : 385.9568 centred at (gu) : 102.6979 91.92010 90.59177 assigned negative charge : -377.4576 centred at (gu) : 102.1119 91.60158 90.95129 start vw surface at 0.1100000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 138064 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21168 grid for indexing accessible points = 1.400000 m= 62289 mr = 100144 m= 18290 mr = 49894 m= 3310 mr = 14043 m= 265 mr = 2320 m= 5 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.7099999 no. cavity mid-points inaccessible to solvent = 6634 time to turn everything in is 1.210000 number of dielectric boundary points 55697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 19398 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) : 1.737179 object centre at (A) : 19.70250 18.04900 12.80700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1752224 7.9211585E-02 midg,1,midg; midg,igrid,midg 0.1720358 0.2039754 1,midg,midg; igrid,midg,midg 5.2815113E-02 -8.1234410E-02 gauss-seidel spectral radius is 0.9991707 estimated iterations to convergence 274 setup time was (sec) 1.570000 now iterating at: 23:15:33 rms-change max change #iterations 8.514174 273.2648 at 10iterations 4.781291 112.4362 at 20iterations 2.671943 69.58891 at 30iterations 1.498749 32.78050 at 40iterations 0.8344656 19.11539 at 50iterations 0.4651842 10.23398 at 60iterations 0.2585308 5.515122 at 70iterations 0.1442156 3.127125 at 80iterations 8.0095559E-02 1.774162 at 90iterations 4.4743214E-02 0.9302063 at 100iterations 2.4902038E-02 0.5139999 at 110iterations 1.3905233E-02 0.2833252 at 120iterations 7.8099472E-03 0.1713486 at 130iterations 4.4174539E-03 0.1009369 at 140iterations 2.5385434E-03 5.9516907E-02 at 150iterations 1.4998098E-03 3.7525177E-02 at 160iterations 9.2080049E-04 2.4623871E-02 at 170iterations 5.9012877E-04 1.6738892E-02 at 180iterations finished qdiffx linear iterations at : 23:15:51 total time elapsed so far: 18.99000 # loops : 180 mean,max change (kT/e) : 5.9012877E-04 1.6738892E-02 energy calculations done at 18.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.15000 DelPhi exited at 23:15:51 19.155u 0.525s 0:19.95 98.5% 0+0k 0+0io 0pf+0w