Wed Nov 2 16:31:15 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 Wed Nov 2 2011 at 16:31:15 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1065 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 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: 0.5568504 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): -9.924999 35.30200 ymin,ymax (A): 0.4000000 42.02600 zmin,zma (A): -17.94900 45.98200 x,y,z range (A): 45.22700 41.62600 63.93100 scale (grids/A): 0.5568504 object centre (A): 12.68850 21.21300 14.01650 number of atom coordinates read : 1965 total number of charged atoms : 1833 net assigned charge : 3.000002 assigned positive charge : 288.1331 centred at (gu) : 89.55635 89.66553 89.99870 assigned negative charge : -285.1333 centred at (gu) : 89.65529 89.82697 90.00191 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4120 nv = 96 ne = 84 npr = 40086 no. pairs analyzed = 40086 no. exposed pairs = 2434 no. arc points = 17009 no. surface atoms = 835 nbur = 1130 mkacc time = 7.9999998E-02 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 = 1.568000 m= 172 mr = 2198 m= 0 mr = 16 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 2078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1811 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 5210 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9844449E-10 2.5744576E-10 midg,1,midg; midg,igrid,midg 1.3934158E-09 -7.0675854E-10 1,midg,midg; igrid,midg,midg 1.0020128E-09 -3.2004274E-10 gauss-seidel spectral radius is 0.9832872 estimated iterations to convergence 64 setup time was (sec) 0.3800000 now iterating at: 16:31:15 rms-change max change #iterations 6.4304993E-02 11.98796 at 10iterations 4.5283874E-03 0.8894129 at 20iterations 3.1130173E-04 6.0235977E-02 at 30iterations 2.2290787E-05 4.8484802E-03 at 40iterations 1.5217065E-06 3.0517578E-04 at 50iterations finished qdiffx linear iterations at : 16:31:18 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.5217065E-06 3.0517578E-04 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 16:31:19 3.498u 0.206s 0:04.06 90.8% 0+0k 1896+45552io 3pf+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 Wed Nov 2 2011 at 16:31:19 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1065 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 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: 1.670551 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): -9.924999 35.30200 ymin,ymax (A): 0.4000000 42.02600 zmin,zma (A): -17.94900 45.98200 x,y,z range (A): 45.22700 41.62600 63.93100 scale (grids/A): 1.670551 object centre (A): 12.68850 21.21300 14.01650 number of atom coordinates read : 1965 total number of charged atoms : 1833 net assigned charge : 3.000002 assigned positive charge : 288.1331 centred at (gu) : 88.66927 88.99674 89.99627 assigned negative charge : -285.1333 centred at (gu) : 88.96618 89.48112 90.00585 start vw surface at 0.1000000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 44780 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17009 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 15211 mr = 30366 m= 1779 mr = 11248 m= 56 mr = 989 m= 0 mr = 5 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 259 time to turn everything in is 0.3000000 number of dielectric boundary points 19218 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 14124 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) : 0.5568504 object centre at (A) : 12.68850 21.21300 14.01650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3011893E-02 1.2766046E-02 midg,1,midg; midg,igrid,midg 2.9255587E-03 -5.1309378E-03 1,midg,midg; igrid,midg,midg 2.2800945E-04 -1.6299471E-03 gauss-seidel spectral radius is 0.9981472 estimated iterations to convergence 185 setup time was (sec) 0.5000000 now iterating at: 16:31:19 rms-change max change #iterations 2.730041 144.2939 at 10iterations 1.121616 51.64557 at 20iterations 0.4646999 23.17078 at 30iterations 0.1914178 8.567115 at 40iterations 7.9447076E-02 3.609947 at 50iterations 3.2672200E-02 1.365244 at 60iterations 1.3507942E-02 0.5491257 at 70iterations 5.5789552E-03 0.2676506 at 80iterations 2.3103161E-03 9.6986413E-02 at 90iterations 9.5137197E-04 4.4921875E-02 at 100iterations 3.9464486E-04 1.5762329E-02 at 110iterations 1.6302496E-04 7.5435638E-03 at 120iterations finished qdiffx linear iterations at : 16:31:27 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.6302496E-04 7.5435638E-03 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 16:31:27 7.790u 0.207s 0:08.51 93.8% 0+0k 0+45144io 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 Wed Nov 2 2011 at 16:31:27 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1065 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 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: 2.505827 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): -9.924999 35.30200 ymin,ymax (A): 0.4000000 42.02600 zmin,zma (A): -17.94900 45.98200 x,y,z range (A): 45.22700 41.62600 63.93100 scale (grids/A): 2.505827 object centre (A): 12.68850 21.21300 14.01650 number of atom coordinates read : 1965 total number of charged atoms : 1833 net assigned charge : 3.000002 assigned positive charge : 288.1331 centred at (gu) : 88.00380 88.49514 89.99439 assigned negative charge : -285.1333 centred at (gu) : 88.44937 89.22172 90.00871 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 103515 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17009 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 50827 mr = 73729 m= 16554 mr = 41513 m= 2994 mr = 13316 m= 219 mr = 2174 m= 5 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 943 time to turn everything in is 0.7300000 number of dielectric boundary points 43293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 14656 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) : 1.670551 object centre at (A) : 12.68850 21.21300 14.01650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1006954 9.7307324E-02 midg,1,midg; midg,igrid,midg 1.7579390E-02 -7.8169398E-02 1,midg,midg; igrid,midg,midg -1.5929705E-02 -3.9794538E-02 gauss-seidel spectral radius is 0.9990888 estimated iterations to convergence 262 setup time was (sec) 0.9500000 now iterating at: 16:31:29 rms-change max change #iterations 6.900010 316.0160 at 10iterations 3.797254 112.9594 at 20iterations 2.065429 57.76238 at 30iterations 1.122633 28.21076 at 40iterations 0.6124396 17.57293 at 50iterations 0.3313320 9.200468 at 60iterations 0.1793136 4.248707 at 70iterations 9.7093083E-02 2.324398 at 80iterations 5.2643634E-02 1.292402 at 90iterations 2.8394613E-02 0.7107024 at 100iterations 1.5288840E-02 0.3846130 at 110iterations 8.2726683E-03 0.1920319 at 120iterations 4.4702641E-03 0.1172097 at 130iterations 2.4131308E-03 6.0251236E-02 at 140iterations 1.3036678E-03 3.4144878E-02 at 150iterations 7.0098287E-04 1.5808105E-02 at 160iterations 3.7873260E-04 8.6181462E-03 at 170iterations 2.0447913E-04 4.7855377E-03 at 180iterations finished qdiffx linear iterations at : 16:31:40 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 2.0447913E-04 4.7855377E-03 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.08000 DelPhi exited at 16:31:40 12.084u 0.215s 0:12.95 94.9% 0+0k 0+45136io 0pf+0w