Sun Oct 9 21:27:58 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 Sun Oct 9 2011 at 21:27:58 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2536 !!! WARNING: GLM 42 has a net charge of -0.6000 !!! WARNING: HIZ 46 has a net charge of 0.2000 !!! WARNING: ZN6 654 has a net charge of 1.4000 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: 0.6513585 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): -11.88500 38.17600 ymin,ymax (A): -22.19300 32.46200 zmin,zma (A): -11.75400 41.71200 x,y,z range (A): 50.06100 54.65500 53.46600 scale (grids/A): 0.6513585 object centre (A): 13.14550 5.134501 14.97900 number of atom coordinates read : 2536 total number of charged atoms : 2429 net assigned charge : 7.500011 assigned positive charge : 389.2779 centred at (gu) : 90.81836 89.65194 90.10928 assigned negative charge : -381.7787 centred at (gu) : 90.80419 89.48873 90.09317 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7366 nv = 96 ne = 84 npr = 48878 no. pairs analyzed = 48878 no. exposed pairs = 3251 no. arc points = 23006 no. surface atoms = 1109 nbur = 1427 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 436 mr = 3967 m= 0 mr = 64 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.3100000 number of dielectric boundary points 3771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2322 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8776 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2354793E-08 1.8038397E-08 midg,1,midg; midg,igrid,midg -1.1586748E-08 3.7248089E-08 1,midg,midg; igrid,midg,midg 1.0977907E-08 2.0515634E-08 gauss-seidel spectral radius is 0.9877872 estimated iterations to convergence 74 setup time was (sec) 0.5800000 now iterating at: 21:27:59 rms-change max change #iterations 0.1537127 22.24505 at 10iterations 1.5809465E-02 2.344459 at 20iterations 1.6388487E-03 0.2220821 at 30iterations 1.7305731E-04 2.8674126E-02 at 40iterations 1.7861281E-05 2.7856827E-03 at 50iterations finished qdiffx linear iterations at : 21:28:02 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 1.7861281E-05 2.7856827E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 21:28:02 3.656u 0.220s 0:04.14 93.4% 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 Sun Oct 9 2011 at 21:28:02 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2536 !!! WARNING: GLM 42 has a net charge of -0.6000 !!! WARNING: HIZ 46 has a net charge of 0.2000 !!! WARNING: ZN6 654 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.954076 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): -11.88500 38.17600 ymin,ymax (A): -22.19300 32.46200 zmin,zma (A): -11.75400 41.71200 x,y,z range (A): 50.06100 54.65500 53.46600 scale (grids/A): 1.954076 object centre (A): 13.14550 5.134501 14.97900 number of atom coordinates read : 2536 total number of charged atoms : 2429 net assigned charge : 7.500011 assigned positive charge : 389.2779 centred at (gu) : 92.45431 88.95532 90.32755 assigned negative charge : -381.7787 centred at (gu) : 92.41249 88.46608 90.27932 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 79414 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23006 grid for indexing accessible points = 1.400000 m= 29609 mr = 54377 m= 5228 mr = 21787 m= 399 mr = 3356 m= 8 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 530 time to turn everything in is 0.6100000 number of dielectric boundary points 34980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19161 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) : 0.6513585 object centre at (A) : 13.14550 5.134501 14.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3870550E-02 -9.9037178E-03 midg,1,midg; midg,igrid,midg 1.7714199E-02 5.5566527E-02 1,midg,midg; igrid,midg,midg -5.8148587E-03 1.6566858E-02 gauss-seidel spectral radius is 0.9986993 estimated iterations to convergence 220 setup time was (sec) 0.9200000 now iterating at: 21:28:04 rms-change max change #iterations 4.390805 179.4171 at 10iterations 2.081771 72.31276 at 20iterations 0.9915069 31.95260 at 30iterations 0.4729405 16.17757 at 40iterations 0.2245546 6.825371 at 50iterations 0.1070544 3.176189 at 60iterations 5.0982840E-02 1.844398 at 70iterations 2.4283748E-02 0.8863831 at 80iterations 1.1566573E-02 0.3543739 at 90iterations 5.5076252E-03 0.1806240 at 100iterations 2.6232253E-03 8.6886406E-02 at 110iterations 1.2533830E-03 4.3075562E-02 at 120iterations finished qdiffx linear iterations at : 21:28:10 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 1.2533830E-03 4.3075562E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 21:28:11 7.710u 0.217s 0:08.21 96.4% 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 Sun Oct 9 2011 at 21:28:11 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2536 !!! WARNING: GLM 42 has a net charge of -0.6000 !!! WARNING: HIZ 46 has a net charge of 0.2000 !!! WARNING: ZN6 654 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.931113 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): -11.88500 38.17600 ymin,ymax (A): -22.19300 32.46200 zmin,zma (A): -11.75400 41.71200 x,y,z range (A): 50.06100 54.65500 53.46600 scale (grids/A): 2.931113 object centre (A): 13.14550 5.134501 14.97900 number of atom coordinates read : 2536 total number of charged atoms : 2429 net assigned charge : 7.500011 assigned positive charge : 389.2779 centred at (gu) : 93.68140 88.43300 90.49113 assigned negative charge : -381.7787 centred at (gu) : 93.61866 87.69902 90.41895 start vw surface at 0.2200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 183326 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23006 grid for indexing accessible points = 1.400000 m= 93977 mr = 131586 m= 35889 mr = 76847 m= 9533 mr = 28776 m= 1703 mr = 7280 m= 163 mr = 1189 m= 6 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1489 time to turn everything in is 1.590000 number of dielectric boundary points 78813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 19432 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) : 1.954076 object centre at (A) : 13.14550 5.134501 14.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2664691 -0.2890631 midg,1,midg; midg,igrid,midg 6.3064836E-02 0.6011961 1,midg,midg; igrid,midg,midg -0.2033784 0.2439347 gauss-seidel spectral radius is 0.9992834 estimated iterations to convergence 295 setup time was (sec) 1.910000 now iterating at: 21:28:13 rms-change max change #iterations 10.22246 389.1027 at 10iterations 5.989280 139.6443 at 20iterations 3.498327 71.21581 at 30iterations 2.036725 40.45157 at 40iterations 1.186134 21.32842 at 50iterations 0.6899843 11.71753 at 60iterations 0.3997382 7.788776 at 70iterations 0.2320296 3.991364 at 80iterations 0.1342988 2.356924 at 90iterations 7.7965900E-02 1.339863 at 100iterations 4.5043804E-02 0.7673059 at 110iterations 2.6113544E-02 0.4746995 at 120iterations 1.5129045E-02 0.2565689 at 130iterations 8.7715276E-03 0.1471024 at 140iterations 5.0604055E-03 9.0514183E-02 at 150iterations 2.9407714E-03 5.3125381E-02 at 160iterations 1.7004353E-03 3.0378819E-02 at 170iterations 9.8317314E-04 1.7015457E-02 at 180iterations finished qdiffx linear iterations at : 21:28:25 total time elapsed so far: 13.85000 # loops : 180 mean,max change (kT/e) : 9.8317314E-04 1.7015457E-02 energy calculations done at 13.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.07000 DelPhi exited at 21:28:25 14.069u 0.218s 0:14.57 97.9% 0+0k 0+0io 0pf+0w