Sat Oct 15 15:37:55 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 Sat Oct 15 2011 at 15:37:55 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3374 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: 0.5840183 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): 0.2720000 48.38500 ymin,ymax (A): -8.514000 52.44300 zmin,zma (A): 2.904000 60.63500 x,y,z range (A): 48.11300 60.95700 57.73100 scale (grids/A): 0.5840183 object centre (A): 24.32850 21.96450 31.76950 number of atom coordinates read : 3374 total number of charged atoms : 3205 net assigned charge : -1.499990 assigned positive charge : 502.9645 centred at (gu) : 89.86167 89.06766 90.11691 assigned negative charge : -504.4658 centred at (gu) : 89.79433 89.06349 90.09927 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7484 nv = 96 ne = 84 npr = 70286 no. pairs analyzed = 70286 no. exposed pairs = 3816 no. arc points = 26142 no. surface atoms = 1298 nbur = 2076 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 = 1.456000 m= 318 mr = 4407 m= 0 mr = 25 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 67 time to turn everything in is 0.2500000 number of dielectric boundary points 3370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2703 ## 295 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5294283E-10 1.3357415E-10 midg,1,midg; midg,igrid,midg -6.0824562E-10 -2.0694398E-10 1,midg,midg; igrid,midg,midg -2.3840268E-09 1.4822293E-09 gauss-seidel spectral radius is 0.9848895 estimated iterations to convergence 67 setup time was (sec) 0.4300000 now iterating at: 15:37:56 rms-change max change #iterations 0.1067484 15.00247 at 10iterations 8.8991178E-03 1.267548 at 20iterations 7.7807374E-04 0.1213188 at 30iterations 9.2463051E-05 1.7976761E-02 at 40iterations 1.4018406E-05 2.6969910E-03 at 50iterations finished qdiffx linear iterations at : 15:38:00 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 1.4018406E-05 2.6969910E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 15:38:01 3.594u 0.204s 0:05.51 68.7% 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 15 2011 at 15:38:01 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3374 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.752055 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): 0.2720000 48.38500 ymin,ymax (A): -8.514000 52.44300 zmin,zma (A): 2.904000 60.63500 x,y,z range (A): 48.11300 60.95700 57.73100 scale (grids/A): 1.752055 object centre (A): 24.32850 21.96450 31.76950 number of atom coordinates read : 3374 total number of charged atoms : 3205 net assigned charge : -1.499990 assigned positive charge : 502.9645 centred at (gu) : 89.58411 87.20200 90.35003 assigned negative charge : -504.4658 centred at (gu) : 89.38260 87.19003 90.29732 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83188 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26142 grid for indexing accessible points = 1.400000 m= 28602 mr = 60291 m= 3356 mr = 21553 m= 112 mr = 2085 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 3985 time to turn everything in is 0.4200000 number of dielectric boundary points 31299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 24873 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) : 0.5840183 object centre at (A) : 24.32850 21.96450 31.76950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3088162E-03 2.5032824E-03 midg,1,midg; midg,igrid,midg -1.7404402E-02 -2.1251991E-02 1,midg,midg; igrid,midg,midg -4.9887779E-03 7.9034467E-04 gauss-seidel spectral radius is 0.9984616 estimated iterations to convergence 202 setup time was (sec) 0.7000000 now iterating at: 15:38:02 rms-change max change #iterations 4.158475 153.8869 at 10iterations 1.852548 64.37051 at 20iterations 0.8308449 25.09352 at 30iterations 0.3726326 11.06225 at 40iterations 0.1673982 5.694626 at 50iterations 7.4904397E-02 2.282763 at 60iterations 3.3662263E-02 1.015555 at 70iterations 1.5034648E-02 0.4596863 at 80iterations 6.7649861E-03 0.2065849 at 90iterations 3.0322336E-03 9.4760418E-02 at 100iterations 1.3674840E-03 3.9737701E-02 at 110iterations 6.1530492E-04 2.1015167E-02 at 120iterations finished qdiffx linear iterations at : 15:38:14 total time elapsed so far: 8.490000 # loops : 120 mean,max change (kT/e) : 6.1530492E-04 2.1015167E-02 energy calculations done at 8.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.620000 DelPhi exited at 15:38:14 8.618u 0.302s 0:13.29 67.0% 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 15 2011 at 15:38:14 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3374 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: 2.628082 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): 0.2720000 48.38500 ymin,ymax (A): -8.514000 52.44300 zmin,zma (A): 2.904000 60.63500 x,y,z range (A): 48.11300 60.95700 57.73100 scale (grids/A): 2.628082 object centre (A): 24.32850 21.96450 31.76950 number of atom coordinates read : 3374 total number of charged atoms : 3205 net assigned charge : -1.499990 assigned positive charge : 502.9645 centred at (gu) : 89.37595 85.80280 90.52484 assigned negative charge : -504.4658 centred at (gu) : 89.07372 85.78491 90.44587 start vw surface at 0.1000000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 193022 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26142 grid for indexing accessible points = 1.400000 m= 96692 mr = 145819 m= 30929 mr = 80766 m= 5792 mr = 25076 m= 497 mr = 4382 m= 13 mr = 297 m= 0 mr = 2 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 13521 time to turn everything in is 1.050000 number of dielectric boundary points 70603 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 25627 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) : 1.752055 object centre at (A) : 24.32850 21.96450 31.76950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3285102E-02 -0.1073548 midg,1,midg; midg,igrid,midg -0.2328106 -0.3247137 1,midg,midg; igrid,midg,midg -4.7005352E-02 -8.0172662E-03 gauss-seidel spectral radius is 0.9992202 estimated iterations to convergence 283 setup time was (sec) 1.310000 now iterating at: 15:38:16 rms-change max change #iterations 10.07373 261.1285 at 10iterations 5.756980 127.0076 at 20iterations 3.279782 70.73692 at 30iterations 1.862325 38.71911 at 40iterations 1.055592 19.34272 at 50iterations 0.5995805 11.35137 at 60iterations 0.3402412 6.192013 at 70iterations 0.1924167 3.552969 at 80iterations 0.1091180 2.057708 at 90iterations 6.1814189E-02 1.317642 at 100iterations 3.4955289E-02 0.6216316 at 110iterations 1.9828640E-02 0.3511581 at 120iterations 1.1208165E-02 0.2325521 at 130iterations 6.3455892E-03 0.1172180 at 140iterations 3.5941952E-03 6.1348915E-02 at 150iterations 2.0317321E-03 3.8906097E-02 at 160iterations 1.1547224E-03 2.0305634E-02 at 170iterations 6.5384025E-04 1.0978699E-02 at 180iterations finished qdiffx linear iterations at : 15:38:36 total time elapsed so far: 14.01000 # loops : 180 mean,max change (kT/e) : 6.5384025E-04 1.0978699E-02 energy calculations done at 14.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.14000 DelPhi exited at 15:38:37 14.140u 0.300s 0:22.92 63.0% 0+0k 0+0io 0pf+0w