Tue Oct 11 03:34:19 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 Tue Oct 11 2011 at 03:34:19 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2262 !!! WARNING: GLU 460 has a net charge of -2.0000 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: 0.5598453 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): -27.62500 35.96400 ymin,ymax (A): -7.047000 41.24600 zmin,zma (A): 4.420000 51.41200 x,y,z range (A): 63.58900 48.29300 46.99200 scale (grids/A): 0.5598453 object centre (A): 4.169500 17.09950 27.91600 number of atom coordinates read : 2262 total number of charged atoms : 2176 net assigned charge : -6.499980 assigned positive charge : 336.4022 centred at (gu) : 92.13065 90.11060 89.97414 assigned negative charge : -342.9027 centred at (gu) : 92.16328 90.18698 89.86311 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4716 nv = 96 ne = 84 npr = 45490 no. pairs analyzed = 45490 no. exposed pairs = 2902 no. arc points = 21059 no. surface atoms = 985 nbur = 1277 mkacc time = 0.1200000 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= 205 mr = 2361 m= 0 mr = 7 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2553 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2116 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6076 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6368846E-09 2.4874428E-10 midg,1,midg; midg,igrid,midg -3.5569474E-11 -1.3627264E-09 1,midg,midg; igrid,midg,midg -2.4873784E-10 -1.5907173E-09 gauss-seidel spectral radius is 0.9834884 estimated iterations to convergence 64 setup time was (sec) 0.5700000 now iterating at: 03:34:20 rms-change max change #iterations 7.0512779E-02 14.10658 at 10iterations 5.0288597E-03 0.9644966 at 20iterations 3.5615126E-04 5.7928085E-02 at 30iterations 2.5270931E-05 5.0106049E-03 at 40iterations 1.7775528E-06 3.5476685E-04 at 50iterations finished qdiffx linear iterations at : 03:34:23 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 1.7775528E-06 3.5476685E-04 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 03:34:24 4.035u 0.266s 0:04.72 90.8% 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 Oct 11 2011 at 03:34:24 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 = 2262 !!! WARNING: GLU 460 has a net charge of -2.0000 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: 1.679536 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): -27.62500 35.96400 ymin,ymax (A): -7.047000 41.24600 zmin,zma (A): 4.420000 51.41200 x,y,z range (A): 63.58900 48.29300 46.99200 scale (grids/A): 1.679536 object centre (A): 4.169500 17.09950 27.91600 number of atom coordinates read : 2262 total number of charged atoms : 2176 net assigned charge : -6.499980 assigned positive charge : 336.4022 centred at (gu) : 96.39143 90.33114 89.92187 assigned negative charge : -342.9027 centred at (gu) : 96.48974 90.56067 89.58933 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 51427 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21059 grid for indexing accessible points = 1.400000 m= 15256 mr = 33915 m= 1563 mr = 10291 m= 43 mr = 785 m= 0 mr = 1 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 103 time to turn everything in is 0.4800000 number of dielectric boundary points 23297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 202 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 16815 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) : 0.5598453 object centre at (A) : 4.169500 17.09950 27.91600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4289538E-03 6.2282141E-03 midg,1,midg; midg,igrid,midg 1.7415686E-03 -1.1157338E-02 1,midg,midg; igrid,midg,midg -2.6100045E-03 -2.3369079E-02 gauss-seidel spectral radius is 0.9982094 estimated iterations to convergence 188 setup time was (sec) 0.7600000 now iterating at: 03:34:25 rms-change max change #iterations 3.040716 133.3183 at 10iterations 1.265872 53.72186 at 20iterations 0.5334577 22.43534 at 30iterations 0.2231802 9.066425 at 40iterations 9.3714111E-02 3.573856 at 50iterations 3.9052162E-02 1.621796 at 60iterations 1.6406743E-02 0.6384602 at 70iterations 6.8530818E-03 0.2617264 at 80iterations 2.8802080E-03 0.1261673 at 90iterations 1.2091066E-03 4.8595428E-02 at 100iterations 5.0545682E-04 2.0959824E-02 at 110iterations 2.1192360E-04 8.0642700E-03 at 120iterations finished qdiffx linear iterations at : 03:34:33 total time elapsed so far: 8.830000 # loops : 120 mean,max change (kT/e) : 2.1192360E-04 8.0642700E-03 energy calculations done at 8.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.010000 DelPhi exited at 03:34:34 9.016u 0.289s 0:09.70 95.7% 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 Tue Oct 11 2011 at 03:34:34 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 = 2262 !!! WARNING: GLU 460 has a net charge of -2.0000 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: 2.519304 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): -27.62500 35.96400 ymin,ymax (A): -7.047000 41.24600 zmin,zma (A): 4.420000 51.41200 x,y,z range (A): 63.58900 48.29300 46.99200 scale (grids/A): 2.519304 object centre (A): 4.169500 17.09950 27.91600 number of atom coordinates read : 2262 total number of charged atoms : 2176 net assigned charge : -6.499980 assigned positive charge : 336.4022 centred at (gu) : 99.58710 90.49670 89.88287 assigned negative charge : -342.9027 centred at (gu) : 99.73442 90.84100 89.38394 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 119630 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21059 grid for indexing accessible points = 1.400000 m= 52557 mr = 83347 m= 15014 mr = 40981 m= 2452 mr = 11273 m= 169 mr = 1620 m= 2 mr = 67 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 371 time to turn everything in is 1.110000 number of dielectric boundary points 52536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 17390 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) : 1.679536 object centre at (A) : 4.169500 17.09950 27.91600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7768746E-02 0.1321589 midg,1,midg; midg,igrid,midg 3.2635547E-02 -0.1493015 1,midg,midg; igrid,midg,midg -0.1055687 -0.2528707 gauss-seidel spectral radius is 0.9991250 estimated iterations to convergence 267 setup time was (sec) 1.420000 now iterating at: 03:34:36 rms-change max change #iterations 7.725025 284.3492 at 10iterations 4.278138 127.1458 at 20iterations 2.354274 55.76537 at 30iterations 1.293852 32.47624 at 40iterations 0.7103989 16.66962 at 50iterations 0.3895801 9.881584 at 60iterations 0.2121786 5.246398 at 70iterations 0.1165054 2.514206 at 80iterations 6.3455746E-02 1.438199 at 90iterations 3.4601480E-02 0.9302826 at 100iterations 1.8873956E-02 0.4105310 at 110iterations 1.0335348E-02 0.2298641 at 120iterations 5.6337696E-03 0.1356692 at 130iterations 3.0750255E-03 6.8823814E-02 at 140iterations 1.6790199E-03 4.0891647E-02 at 150iterations 9.1538235E-04 2.0572662E-02 at 160iterations 5.0021429E-04 1.0962486E-02 at 170iterations 2.7266130E-04 6.1182976E-03 at 180iterations finished qdiffx linear iterations at : 03:34:49 total time elapsed so far: 14.40000 # loops : 180 mean,max change (kT/e) : 2.7266130E-04 6.1182976E-03 energy calculations done at 14.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.58000 DelPhi exited at 03:34:49 14.585u 0.298s 0:15.42 96.4% 0+0k 0+0io 0pf+0w