Sat Oct 8 17:44:15 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+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 Sat Oct 8 2011 at 17:44:15 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 # of charge parameter records: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3527 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5257794 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): -1.055000 44.25000 ymin,ymax (A): -30.59500 26.23300 zmin,zma (A): 1.382000 69.09100 x,y,z range (A): 45.30500 56.82800 67.70900 scale (grids/A): 0.5257794 object centre (A): 21.59750 -2.181001 35.23650 number of atom coordinates read : 3527 total number of charged atoms : 3380 net assigned charge : -5.871982 assigned positive charge : 541.8540 centred at (gu) : 90.48855 91.78511 90.58323 assigned negative charge : -547.7280 centred at (gu) : 90.44428 91.74256 90.57788 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6135 nv = 96 ne = 84 npr = 71992 no. pairs analyzed = 71992 no. exposed pairs = 4251 no. arc points = 29259 no. surface atoms = 1436 nbur = 2091 mkacc time = 0.2000000 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 = 1.624000 m= 217 mr = 3278 m= 0 mr = 10 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2954 ## 437 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8220 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5938674E-10 -1.6709316E-10 midg,1,midg; midg,igrid,midg -2.0636061E-10 -5.7687479E-12 1,midg,midg; igrid,midg,midg -2.9156652E-10 2.8420547E-13 gauss-seidel spectral radius is 0.9813991 estimated iterations to convergence 61 setup time was (sec) 0.7000000 now iterating at: 17:44:16 rms-change max change #iterations 6.7809865E-02 9.839647 at 10iterations 4.2205770E-03 0.6368771 at 20iterations 3.6666464E-04 6.1069489E-02 at 30iterations 6.7234723E-05 1.1017323E-02 at 40iterations 1.6533932E-05 2.5682449E-03 at 50iterations finished qdiffx linear iterations at : 17:44:19 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 1.6533932E-05 2.5682449E-03 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.300000 DelPhi exited at 17:44:20 4.299u 0.286s 0:04.86 94.0% 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 17:44:20 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3527 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.577338 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): -1.055000 44.25000 ymin,ymax (A): -30.59500 26.23300 zmin,zma (A): 1.382000 69.09100 x,y,z range (A): 45.30500 56.82800 67.70900 scale (grids/A): 1.577338 object centre (A): 21.59750 -2.181001 35.23650 number of atom coordinates read : 3527 total number of charged atoms : 3380 net assigned charge : -5.871982 assigned positive charge : 541.8540 centred at (gu) : 91.46468 95.35428 91.74840 assigned negative charge : -547.7280 centred at (gu) : 91.33252 95.22734 91.73327 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 69161 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29259 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20736 mr = 48290 m= 1883 mr = 14134 m= 42 mr = 848 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 180 time to turn everything in is 0.6300000 number of dielectric boundary points 28550 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 393 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 25603 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) : 0.5257794 object centre at (A) : 21.59750 -2.181001 35.23650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0413626E-03 1.1472884E-02 midg,1,midg; midg,igrid,midg -8.0842655E-03 -1.1864860E-02 1,midg,midg; igrid,midg,midg -4.3096370E-03 1.3120247E-03 gauss-seidel spectral radius is 0.9980903 estimated iterations to convergence 182 setup time was (sec) 0.9300000 now iterating at: 17:44:21 rms-change max change #iterations 3.468679 194.7756 at 10iterations 1.411481 62.29272 at 20iterations 0.5780337 20.21285 at 30iterations 0.2353795 7.920748 at 40iterations 9.6026354E-02 3.131652 at 50iterations 3.9401427E-02 1.424406 at 60iterations 1.6133659E-02 0.5325508 at 70iterations 6.6379034E-03 0.2280779 at 80iterations 2.7418241E-03 9.8868370E-02 at 90iterations 1.1642029E-03 4.1837692E-02 at 100iterations 5.1314197E-04 2.0713806E-02 at 110iterations 2.4289558E-04 9.1617107E-03 at 120iterations finished qdiffx linear iterations at : 17:44:29 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 2.4289558E-04 9.1617107E-03 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 17:44:30 9.656u 0.339s 0:10.32 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 Sat Oct 8 2011 at 17:44:30 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3527 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.366008 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): -1.055000 44.25000 ymin,ymax (A): -30.59500 26.23300 zmin,zma (A): 1.382000 69.09100 x,y,z range (A): 45.30500 56.82800 67.70900 scale (grids/A): 2.366008 object centre (A): 21.59750 -2.181001 35.23650 number of atom coordinates read : 3527 total number of charged atoms : 3380 net assigned charge : -5.871982 assigned positive charge : 541.8540 centred at (gu) : 92.19657 98.03097 92.62231 assigned negative charge : -547.7280 centred at (gu) : 91.99873 97.84091 92.59995 start vw surface at 0.1900000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 161168 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29259 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 73687 mr = 118311 m= 19292 mr = 58263 m= 2718 mr = 14261 m= 153 mr = 1711 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 558 time to turn everything in is 1.530000 number of dielectric boundary points 64417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 26963 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) : 1.577338 object centre at (A) : 21.59750 -2.181001 35.23650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1915046 9.7564816E-02 midg,1,midg; midg,igrid,midg -0.1139009 -0.1437696 1,midg,midg; igrid,midg,midg -7.5906307E-02 4.6515781E-02 gauss-seidel spectral radius is 0.9991138 estimated iterations to convergence 265 setup time was (sec) 1.860000 now iterating at: 17:44:32 rms-change max change #iterations 9.103542 272.1186 at 10iterations 5.065379 136.1277 at 20iterations 2.807974 62.08921 at 30iterations 1.543622 35.36724 at 40iterations 0.8486592 17.54335 at 50iterations 0.4648101 10.14918 at 60iterations 0.2549036 5.195755 at 70iterations 0.1390120 2.804178 at 80iterations 7.5937375E-02 1.911018 at 90iterations 4.1493163E-02 0.8385081 at 100iterations 2.2639871E-02 0.4430294 at 110iterations 1.2380315E-02 0.2683554 at 120iterations 6.7499722E-03 0.1405368 at 130iterations 3.6823140E-03 8.1572533E-02 at 140iterations 2.0079277E-03 4.5897484E-02 at 150iterations 1.1002475E-03 2.1549225E-02 at 160iterations 6.0439471E-04 1.2104034E-02 at 170iterations 3.3450522E-04 7.4844360E-03 at 180iterations finished qdiffx linear iterations at : 17:44:46 total time elapsed so far: 16.09000 # loops : 180 mean,max change (kT/e) : 3.3450522E-04 7.4844360E-03 energy calculations done at 16.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.27000 DelPhi exited at 17:44:47 16.272u 0.338s 0:16.89 98.2% 0+0k 0+0io 0pf+0w