Mon Oct 10 11:09:06 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 11:09:06 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5526 !!! WARNING: HIR 734 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5075418 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): -19.65800 47.09500 ymin,ymax (A): -13.36500 56.77700 zmin,zma (A): -20.01500 45.44000 x,y,z range (A): 66.75300 70.14200 65.45500 scale (grids/A): 0.5075418 object centre (A): 13.71850 21.70600 12.71250 number of atom coordinates read : 5526 total number of charged atoms : 5369 net assigned charge : 11.01405 assigned positive charge : 881.1888 centred at (gu) : 91.18231 87.62742 88.91911 assigned negative charge : -870.1831 centred at (gu) : 91.17079 87.59889 88.95435 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8998 nv = 96 ne = 84 npr = 108752 no. pairs analyzed = 108752 no. exposed pairs = 6713 no. arc points = 45822 no. surface atoms = 2253 nbur = 3273 mkacc time = 0.2900000 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= 303 mr = 4869 m= 0 mr = 15 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.5600000 number of dielectric boundary points 4417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4506 ## 695 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 12136 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0772487E-10 2.9864458E-11 midg,1,midg; midg,igrid,midg 1.0119569E-10 1.1553822E-10 1,midg,midg; igrid,midg,midg 7.6889835E-11 2.2712497E-10 gauss-seidel spectral radius is 0.9801940 estimated iterations to convergence 59 setup time was (sec) 0.9300000 now iterating at: 11:09:07 rms-change max change #iterations 7.2232246E-02 10.96529 at 10iterations 4.4704382E-03 0.6133480 at 20iterations 9.9217845E-04 0.1391182 at 30iterations 4.8639489E-04 7.2250366E-02 at 40iterations 2.4864305E-04 3.7623405E-02 at 50iterations finished qdiffx linear iterations at : 11:09:11 total time elapsed so far: 5.090000 # loops : 50 mean,max change (kT/e) : 2.4864305E-04 3.7623405E-02 energy calculations done at 5.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.250000 DelPhi exited at 11:09:12 5.251u 0.444s 0:05.96 95.4% 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 Mon Oct 10 2011 at 11:09:12 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5526 !!! WARNING: HIR 734 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.522626 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): -19.65800 47.09500 ymin,ymax (A): -13.36500 56.77700 zmin,zma (A): -20.01500 45.44000 x,y,z range (A): 66.75300 70.14200 65.45500 scale (grids/A): 1.522626 object centre (A): 13.71850 21.70600 12.71250 number of atom coordinates read : 5526 total number of charged atoms : 5369 net assigned charge : 11.01405 assigned positive charge : 881.1888 centred at (gu) : 93.54543 82.88033 86.75548 assigned negative charge : -870.1831 centred at (gu) : 93.51234 82.79665 86.86337 start vw surface at 0.1900000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 103406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45822 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 30012 mr = 73196 m= 2453 mr = 20288 m= 50 mr = 1030 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 1377 time to turn everything in is 0.8600000 number of dielectric boundary points 41407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 638 ## 10 charges are in solution ## iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 40095 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) : 0.5075418 object centre at (A) : 13.71850 21.70600 12.71250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7050060E-03 -2.9698348E-02 midg,1,midg; midg,igrid,midg 3.2272958E-03 5.8264956E-03 1,midg,midg; igrid,midg,midg 1.9324007E-02 1.7024104E-02 gauss-seidel spectral radius is 0.9981340 estimated iterations to convergence 184 setup time was (sec) 1.250000 now iterating at: 11:09:14 rms-change max change #iterations 4.191092 152.2323 at 10iterations 1.726019 53.90261 at 20iterations 0.7157172 21.70249 at 30iterations 0.2950176 9.163614 at 40iterations 0.1218616 3.549221 at 50iterations 5.0370138E-02 1.654401 at 60iterations 2.0860109E-02 0.6339769 at 70iterations 8.7445807E-03 0.2528191 at 80iterations 3.7293141E-03 0.1224751 at 90iterations 1.7335707E-03 5.9537888E-02 at 100iterations 9.4235293E-04 3.4373760E-02 at 110iterations 6.2152278E-04 2.0901680E-02 at 120iterations finished qdiffx linear iterations at : 11:09:24 total time elapsed so far: 11.96000 # loops : 120 mean,max change (kT/e) : 6.2152278E-04 2.0901680E-02 energy calculations done at 11.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.13000 DelPhi exited at 11:09:25 12.132u 0.488s 0:13.04 96.7% 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 11:09:25 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5526 !!! WARNING: HIR 734 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.283938 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): -19.65800 47.09500 ymin,ymax (A): -13.36500 56.77700 zmin,zma (A): -20.01500 45.44000 x,y,z range (A): 66.75300 70.14200 65.45500 scale (grids/A): 2.283938 object centre (A): 13.71850 21.70600 12.71250 number of atom coordinates read : 5526 total number of charged atoms : 5369 net assigned charge : 11.01405 assigned positive charge : 881.1888 centred at (gu) : 95.31776 79.32024 85.13259 assigned negative charge : -870.1831 centred at (gu) : 95.26871 79.19511 85.29505 start vw surface at 0.1900000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 241554 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45822 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 108809 mr = 179634 m= 26655 mr = 86046 m= 3498 mr = 19457 m= 146 mr = 2018 m= 7 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 4592 time to turn everything in is 2.080000 number of dielectric boundary points 93480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 2.250000 number of grid points assigned charge 42809 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) : 1.522626 object centre at (A) : 13.71850 21.70600 12.71250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0530592E-02 -0.6392875 midg,1,midg; midg,igrid,midg -6.8166144E-02 6.0377214E-02 1,midg,midg; igrid,midg,midg 0.4456858 0.3471139 gauss-seidel spectral radius is 0.9991688 estimated iterations to convergence 274 setup time was (sec) 2.470000 now iterating at: 11:09:28 rms-change max change #iterations 11.25029 245.1026 at 10iterations 6.429162 138.4708 at 20iterations 3.641476 72.59367 at 30iterations 2.058343 43.66728 at 40iterations 1.158199 22.65912 at 50iterations 0.6496683 13.09974 at 60iterations 0.3638085 6.709806 at 70iterations 0.2034333 3.697703 at 80iterations 0.1135258 2.293240 at 90iterations 6.3456446E-02 1.123015 at 100iterations 3.5332959E-02 0.5944643 at 110iterations 1.9702356E-02 0.3632030 at 120iterations 1.0981377E-02 0.1910590 at 130iterations 6.1255777E-03 0.1148624 at 140iterations 3.4238205E-03 5.7793140E-02 at 150iterations 1.9175600E-03 3.3472061E-02 at 160iterations 1.0860907E-03 2.0452499E-02 at 170iterations 6.2501809E-04 1.1741638E-02 at 180iterations finished qdiffx linear iterations at : 11:09:47 total time elapsed so far: 21.30000 # loops : 180 mean,max change (kT/e) : 6.2501809E-04 1.1741638E-02 energy calculations done at 21.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.44000 DelPhi exited at 11:09:47 21.448u 0.554s 0:22.34 98.4% 0+0k 0+0io 0pf+0w