Mon Oct 10 16:03:58 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 Mon Oct 10 2011 at 16:03:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4292 !!! WARNING: ASP 607 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5504700 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): -59.22400 -7.739000 ymin,ymax (A): -34.25600 29.56200 zmin,zma (A): -29.18400 35.48800 x,y,z range (A): 51.48500 63.81800 64.67200 scale (grids/A): 0.5504700 object centre (A): -33.48150 -2.347000 3.152001 number of atom coordinates read : 4292 total number of charged atoms : 4191 net assigned charge : 2.500011 assigned positive charge : 647.9430 centred at (gu) : 90.15613 90.24031 88.64902 assigned negative charge : -645.4463 centred at (gu) : 90.17775 90.27684 88.60548 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8484 nv = 96 ne = 84 npr = 86060 no. pairs analyzed = 86060 no. exposed pairs = 5331 no. arc points = 36591 no. surface atoms = 1796 nbur = 2496 mkacc time = 0.1600000 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 = 1.568000 m= 352 mr = 4627 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3783 ## 503 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 11256 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3150872E-10 4.9334659E-10 midg,1,midg; midg,igrid,midg 5.7284255E-10 -2.3779326E-10 1,midg,midg; igrid,midg,midg 4.2290210E-10 -5.5025658E-11 gauss-seidel spectral radius is 0.9830817 estimated iterations to convergence 63 setup time was (sec) 0.5000000 now iterating at: 16:03:59 rms-change max change #iterations 9.3202300E-02 13.45237 at 10iterations 6.7401598E-03 0.8193369 at 20iterations 9.1366691E-04 0.1685352 at 30iterations 3.1349043E-04 5.0605774E-02 at 40iterations 1.2747268E-04 1.7173767E-02 at 50iterations finished qdiffx linear iterations at : 16:04:02 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 1.2747268E-04 1.7173767E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 16:04:02 3.552u 0.188s 0:04.04 92.3% 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 Mon Oct 10 2011 at 16:04:03 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 = 4292 !!! WARNING: ASP 607 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.651410 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): -59.22400 -7.739000 ymin,ymax (A): -34.25600 29.56200 zmin,zma (A): -29.18400 35.48800 x,y,z range (A): 51.48500 63.81800 64.67200 scale (grids/A): 1.651410 object centre (A): -33.48150 -2.347000 3.152001 number of atom coordinates read : 4292 total number of charged atoms : 4191 net assigned charge : 2.500011 assigned positive charge : 647.9430 centred at (gu) : 90.46688 90.71992 85.94551 assigned negative charge : -645.4463 centred at (gu) : 90.53298 90.82983 85.81602 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 94922 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36591 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30976 mr = 66947 m= 3472 mr = 21544 m= 90 mr = 1829 m= 0 mr = 11 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 321 time to turn everything in is 0.4600000 number of dielectric boundary points 39129 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 398 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 32163 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) : 0.5504700 object centre at (A) : -33.48150 -2.347000 3.152001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6215688E-03 -5.8086975E-03 midg,1,midg; midg,igrid,midg 1.8849432E-02 1.5018315E-02 1,midg,midg; igrid,midg,midg -1.7048698E-03 -2.2568653E-04 gauss-seidel spectral radius is 0.9983656 estimated iterations to convergence 196 setup time was (sec) 0.6800000 now iterating at: 16:04:03 rms-change max change #iterations 4.200639 155.5344 at 10iterations 1.837730 61.60873 at 20iterations 0.8021842 24.18032 at 30iterations 0.3507005 12.22635 at 40iterations 0.1529904 4.969066 at 50iterations 6.6983312E-02 2.049692 at 60iterations 2.9416777E-02 0.9202423 at 70iterations 1.2949165E-02 0.4404321 at 80iterations 5.7284683E-03 0.1825695 at 90iterations 2.6143570E-03 8.1882477E-02 at 100iterations 1.2519064E-03 3.6015511E-02 at 110iterations 6.6875434E-04 2.2689819E-02 at 120iterations finished qdiffx linear iterations at : 16:04:11 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 6.6875434E-04 2.2689819E-02 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 16:04:11 8.121u 0.256s 0:08.87 94.3% 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 Mon Oct 10 2011 at 16:04:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4292 !!! WARNING: ASP 607 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.477115 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): -59.22400 -7.739000 ymin,ymax (A): -34.25600 29.56200 zmin,zma (A): -29.18400 35.48800 x,y,z range (A): 51.48500 63.81800 64.67200 scale (grids/A): 2.477115 object centre (A): -33.48150 -2.347000 3.152001 number of atom coordinates read : 4292 total number of charged atoms : 4191 net assigned charge : 2.500011 assigned positive charge : 647.9430 centred at (gu) : 90.69991 91.07955 83.91799 assigned negative charge : -645.4463 centred at (gu) : 90.79914 91.24471 83.72389 start vw surface at 0.1300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 221185 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36591 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 105526 mr = 163928 m= 31489 mr = 84120 m= 5492 mr = 23934 m= 434 mr = 3804 m= 8 mr = 193 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 1013 time to turn everything in is 1.160000 number of dielectric boundary points 88155 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 33489 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) : 1.651410 object centre at (A) : -33.48150 -2.347000 3.152001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3122941 -0.1268546 midg,1,midg; midg,igrid,midg 0.2707374 0.3090153 1,midg,midg; igrid,midg,midg -7.3961266E-03 7.6072901E-03 gauss-seidel spectral radius is 0.9992288 estimated iterations to convergence 284 setup time was (sec) 1.410000 now iterating at: 16:04:13 rms-change max change #iterations 10.90257 300.8858 at 10iterations 6.396522 163.3282 at 20iterations 3.741265 82.38521 at 30iterations 2.170343 49.92126 at 40iterations 1.254755 25.10614 at 50iterations 0.7244188 13.90045 at 60iterations 0.4166154 7.204195 at 70iterations 0.2391769 4.209993 at 80iterations 0.1370656 2.504029 at 90iterations 7.8632966E-02 1.408958 at 100iterations 4.4876035E-02 0.8773470 at 110iterations 2.5714615E-02 0.4613106 at 120iterations 1.4771174E-02 0.2800293 at 130iterations 8.4862970E-03 0.1603050 at 140iterations 4.9161036E-03 9.8031998E-02 at 150iterations 2.8887470E-03 4.9219131E-02 at 160iterations 1.7441305E-03 3.1669617E-02 at 170iterations 1.0989475E-03 2.0103455E-02 at 180iterations finished qdiffx linear iterations at : 16:04:26 total time elapsed so far: 14.36000 # loops : 180 mean,max change (kT/e) : 1.0989475E-03 2.0103455E-02 energy calculations done at 14.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.49000 DelPhi exited at 16:04:26 14.492u 0.260s 0:15.05 98.0% 0+0k 0+0io 0pf+0w