Mon Oct 10 17:04:14 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 Mon Oct 10 2011 at 17:04:14 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4854 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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: 0.5117958 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): -18.88500 36.90500 ymin,ymax (A): -30.64300 35.35200 zmin,zma (A): -4.040000 65.51900 x,y,z range (A): 55.79000 65.99500 69.55900 scale (grids/A): 0.5117958 object centre (A): 9.010001 2.354501 30.73950 number of atom coordinates read : 4854 total number of charged atoms : 4603 net assigned charge : 7.706046 assigned positive charge : 730.1442 centred at (gu) : 90.35114 90.27874 88.48740 assigned negative charge : -722.4428 centred at (gu) : 90.22502 90.30315 88.46167 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8040 nv = 96 ne = 84 npr = 97917 no. pairs analyzed = 97917 no. exposed pairs = 6132 no. arc points = 42374 no. surface atoms = 2068 nbur = 2786 mkacc time = 0.2400000 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 = 1.652000 m= 285 mr = 4134 m= 0 mr = 7 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4110 ## 592 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 10667 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3307998E-11 1.2594521E-10 midg,1,midg; midg,igrid,midg 1.6960482E-10 5.1120715E-11 1,midg,midg; igrid,midg,midg -2.1627745E-10 5.0134635E-10 gauss-seidel spectral radius is 0.9804815 estimated iterations to convergence 59 setup time was (sec) 0.7700000 now iterating at: 17:04:15 rms-change max change #iterations 6.9669247E-02 9.127543 at 10iterations 4.7503407E-03 0.7203175 at 20iterations 8.0006459E-04 0.1005325 at 30iterations 2.7576095E-04 3.3991575E-02 at 40iterations 1.0730735E-04 1.5328765E-02 at 50iterations finished qdiffx linear iterations at : 17:04:18 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 1.0730735E-04 1.5328765E-02 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.840000 DelPhi exited at 17:04:21 3.848u 0.232s 0:07.03 57.8% 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 Mon Oct 10 2011 at 17:04:21 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4854 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.535387 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): -18.88500 36.90500 ymin,ymax (A): -30.64300 35.35200 zmin,zma (A): -4.040000 65.51900 x,y,z range (A): 55.79000 65.99500 69.55900 scale (grids/A): 1.535387 object centre (A): 9.010001 2.354501 30.73950 number of atom coordinates read : 4854 total number of charged atoms : 4603 net assigned charge : 7.706046 assigned positive charge : 730.1442 centred at (gu) : 91.05195 90.83496 85.46062 assigned negative charge : -722.4428 centred at (gu) : 90.67468 90.90919 85.38454 start vw surface at 0.2000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 91037 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42374 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25876 mr = 62467 m= 2172 mr = 16734 m= 60 mr = 897 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 39046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 512 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 34591 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) : 0.5117958 object centre at (A) : 9.010001 2.354501 30.73950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1878995E-03 1.9304525E-02 midg,1,midg; midg,igrid,midg 1.9260148E-03 -1.0281982E-02 1,midg,midg; igrid,midg,midg -6.3541072E-04 1.4438046E-02 gauss-seidel spectral radius is 0.9981315 estimated iterations to convergence 184 setup time was (sec) 1.040000 now iterating at: 17:04:23 rms-change max change #iterations 3.835187 141.3197 at 10iterations 1.573820 51.61912 at 20iterations 0.6499155 20.57207 at 30iterations 0.2688581 9.142179 at 40iterations 0.1107588 3.577530 at 50iterations 4.5622192E-02 1.487602 at 60iterations 1.8847771E-02 0.5974617 at 70iterations 7.8632729E-03 0.2644501 at 80iterations 3.3112618E-03 0.1018524 at 90iterations 1.4268660E-03 4.5417786E-02 at 100iterations 6.5822719E-04 2.1198273E-02 at 110iterations 3.4052110E-04 1.0572433E-02 at 120iterations finished qdiffx linear iterations at : 17:04:30 total time elapsed so far: 8.270000 # loops : 120 mean,max change (kT/e) : 3.4052110E-04 1.0572433E-02 energy calculations done at 8.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.480000 DelPhi exited at 17:04:31 8.478u 0.256s 0:09.66 90.2% 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 17:04:31 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4854 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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: 2.303081 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): -18.88500 36.90500 ymin,ymax (A): -30.64300 35.35200 zmin,zma (A): -4.040000 65.51900 x,y,z range (A): 55.79000 65.99500 69.55900 scale (grids/A): 2.303081 object centre (A): 9.010001 2.354501 30.73950 number of atom coordinates read : 4854 total number of charged atoms : 4603 net assigned charge : 7.706046 assigned positive charge : 730.1442 centred at (gu) : 91.57761 91.25199 83.19060 assigned negative charge : -722.4428 centred at (gu) : 91.01201 91.36373 83.07665 start vw surface at 0.2200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 212480 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42374 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 93440 mr = 153599 m= 22944 mr = 72378 m= 3146 mr = 16017 m= 179 mr = 1815 m= 1 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.660000 number of dielectric boundary points 88324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 36721 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) : 1.535387 object centre at (A) : 9.010001 2.354501 30.73950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1233921 0.4796931 midg,1,midg; midg,igrid,midg -9.2180729E-02 -0.2831787 1,midg,midg; igrid,midg,midg 3.0247460E-03 0.2176441 gauss-seidel spectral radius is 0.9991711 estimated iterations to convergence 274 setup time was (sec) 2.000000 now iterating at: 17:04:33 rms-change max change #iterations 10.44886 270.0547 at 10iterations 6.033807 140.8467 at 20iterations 3.448189 82.49789 at 30iterations 1.959690 43.76711 at 40iterations 1.110208 23.91590 at 50iterations 0.6275250 14.32792 at 60iterations 0.3525643 7.063595 at 70iterations 0.1980990 3.853455 at 80iterations 0.1109432 2.469980 at 90iterations 6.2164564E-02 1.296696 at 100iterations 3.4739941E-02 0.6876814 at 110iterations 1.9407297E-02 0.3550749 at 120iterations 1.0854096E-02 0.2086201 at 130iterations 6.0683060E-03 0.1069221 at 140iterations 3.3842449E-03 6.8510056E-02 at 150iterations 1.8947978E-03 3.4646988E-02 at 160iterations 1.0624714E-03 2.0322800E-02 at 170iterations 6.0003542E-04 1.1528015E-02 at 180iterations finished qdiffx linear iterations at : 17:04:46 total time elapsed so far: 15.10000 # loops : 180 mean,max change (kT/e) : 6.0003542E-04 1.1528015E-02 energy calculations done at 15.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.29000 DelPhi exited at 17:04:48 15.291u 0.251s 0:16.68 93.1% 0+0k 0+0io 0pf+0w