Tue Nov 22 14:10:03 PST 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 Tue Nov 22 2011 at 14:10:09 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5763035 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): -34.96900 10.21100 ymin,ymax (A): 1.151000 41.03400 zmin,zma (A): -3.042000 58.73100 x,y,z range (A): 45.18000 39.88300 61.77300 scale (grids/A): 0.5763035 object centre (A): -12.37900 21.09250 27.84450 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.35275 89.60403 89.93167 assigned negative charge : -284.8263 centred at (gu) : 90.26749 89.72923 89.91611 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4246 nv = 96 ne = 84 npr = 40694 no. pairs analyzed = 40694 no. exposed pairs = 2472 no. arc points = 17347 no. surface atoms = 844 nbur = 1120 mkacc time = 7.0000008E-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 = 1.512000 m= 194 mr = 2258 m= 0 mr = 15 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.1500000 number of dielectric boundary points 2167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1771 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5409 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7783693E-10 7.4873263E-10 midg,1,midg; midg,igrid,midg 2.3133739E-09 -9.2475655E-10 1,midg,midg; igrid,midg,midg -4.6490331E-10 1.7607366E-09 gauss-seidel spectral radius is 0.9843758 estimated iterations to convergence 66 setup time was (sec) 0.3500000 now iterating at: 14:10:13 rms-change max change #iterations 7.1616486E-02 12.81027 at 10iterations 5.5444688E-03 1.050497 at 20iterations 4.2564762E-04 7.3213577E-02 at 30iterations 3.1858621E-05 5.5112839E-03 at 40iterations 2.4614676E-06 4.7874451E-04 at 50iterations finished qdiffx linear iterations at : 14:10:23 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 2.4614676E-06 4.7874451E-04 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 14:10:26 3.761u 0.245s 0:17.29 23.1% 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 Nov 22 2011 at 14:10:27 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.728911 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): -34.96900 10.21100 ymin,ymax (A): 1.151000 41.03400 zmin,zma (A): -3.042000 58.73100 x,y,z range (A): 45.18000 39.88300 61.77300 scale (grids/A): 1.728911 object centre (A): -12.37900 21.09250 27.84450 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 91.05801 88.81206 89.79514 assigned negative charge : -284.8263 centred at (gu) : 90.80252 89.18800 89.74846 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 46349 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17347 grid for indexing accessible points = 1.400000 m= 15297 mr = 31205 m= 1826 mr = 11115 m= 59 mr = 1065 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 1394 time to turn everything in is 0.2500000 number of dielectric boundary points 20132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 14210 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) : 0.5763035 object centre at (A) : -12.37900 21.09250 27.84450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1445991E-02 2.3335541E-02 midg,1,midg; midg,igrid,midg 3.3531233E-03 -6.0625346E-03 1,midg,midg; igrid,midg,midg -1.6328711E-03 -1.3369179E-03 gauss-seidel spectral radius is 0.9982638 estimated iterations to convergence 191 setup time was (sec) 0.4900000 now iterating at: 14:10:32 rms-change max change #iterations 2.944695 164.5047 at 10iterations 1.238075 65.11372 at 20iterations 0.5273089 21.45651 at 30iterations 0.2247313 9.327656 at 40iterations 9.5307007E-02 4.200335 at 50iterations 4.0456310E-02 1.572564 at 60iterations 1.7177461E-02 0.6885457 at 70iterations 7.3079593E-03 0.2986221 at 80iterations 3.1145848E-03 0.1179771 at 90iterations 1.3202507E-03 6.2657833E-02 at 100iterations 5.6016468E-04 2.4312973E-02 at 110iterations 2.3846363E-04 9.9172592E-03 at 120iterations finished qdiffx linear iterations at : 14:10:57 total time elapsed so far: 8.690000 # loops : 120 mean,max change (kT/e) : 2.3846363E-04 9.9172592E-03 energy calculations done at 8.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.820000 DelPhi exited at 14:10:58 8.821u 0.263s 0:31.50 28.8% 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 Nov 22 2011 at 14:11:01 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.593366 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): -34.96900 10.21100 ymin,ymax (A): 1.151000 41.03400 zmin,zma (A): -3.042000 58.73100 x,y,z range (A): 45.18000 39.88300 61.77300 scale (grids/A): 2.593366 object centre (A): -12.37900 21.09250 27.84450 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 91.58714 88.21807 89.69269 assigned negative charge : -284.8263 centred at (gu) : 91.20373 88.78210 89.62280 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 107475 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17347 grid for indexing accessible points = 1.400000 m= 50810 mr = 75895 m= 16497 mr = 41142 m= 3124 mr = 13293 m= 308 mr = 2270 m= 6 mr = 198 m= 0 mr = 2 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 4537 time to turn everything in is 0.6500000 number of dielectric boundary points 45420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 14652 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) : 1.728911 object centre at (A) : -12.37900 21.09250 27.84450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2366381 0.2504744 midg,1,midg; midg,igrid,midg 1.7642550E-02 -9.1824636E-02 1,midg,midg; igrid,midg,midg -4.0518627E-02 -4.8915468E-02 gauss-seidel spectral radius is 0.9991280 estimated iterations to convergence 268 setup time was (sec) 0.9600000 now iterating at: 14:11:07 rms-change max change #iterations 7.225132 284.5414 at 10iterations 3.991771 127.0004 at 20iterations 2.189587 59.16444 at 30iterations 1.201280 27.95490 at 40iterations 0.6579278 15.22906 at 50iterations 0.3587725 8.822367 at 60iterations 0.1958243 4.707005 at 70iterations 0.1072919 2.679050 at 80iterations 5.8421064E-02 1.352366 at 90iterations 3.1964436E-02 0.7578335 at 100iterations 1.7413892E-02 0.4016933 at 110iterations 9.5501747E-03 0.2180252 at 120iterations 5.2083568E-03 0.1166754 at 130iterations 2.8424633E-03 6.6902161E-02 at 140iterations 1.5504722E-03 3.7367344E-02 at 150iterations 8.4869354E-04 1.9121170E-02 at 160iterations 4.6305917E-04 1.0277748E-02 at 170iterations 2.5272911E-04 6.0062408E-03 at 180iterations finished qdiffx linear iterations at : 14:11:44 total time elapsed so far: 13.33000 # loops : 180 mean,max change (kT/e) : 2.5272911E-04 6.0062408E-03 energy calculations done at 13.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.46000 DelPhi exited at 14:11:45 13.462u 0.313s 0:44.63 30.8% 0+0k 0+0io 0pf+0w