Tue Oct 11 05:19:35 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 05:19:35 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2305 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: ZN6 650 has a net charge of 1.4000 !!! WARNING: ZN6 651 has a net charge of 1.4000 !!! WARNING: ZN6 652 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6898422 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): 15.69200 63.03500 ymin,ymax (A): -3.547000 33.92600 zmin,zma (A): 20.16900 71.77500 x,y,z range (A): 47.34300 37.47300 51.60600 scale (grids/A): 0.6898422 object centre (A): 39.36350 15.18950 45.97200 number of atom coordinates read : 2305 total number of charged atoms : 1983 net assigned charge : 10.40001 assigned positive charge : 325.3839 centred at (gu) : 91.42934 89.67605 89.22031 assigned negative charge : -314.9841 centred at (gu) : 91.52525 89.61680 89.09843 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6776 nv = 96 ne = 84 npr = 42274 no. pairs analyzed = 42274 no. exposed pairs = 2583 no. arc points = 17745 no. surface atoms = 879 nbur = 1426 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 445 mr = 3888 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1728 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7699 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9409326E-08 8.4246643E-08 midg,1,midg; midg,igrid,midg 4.0690185E-08 7.2967495E-08 1,midg,midg; igrid,midg,midg 6.7910790E-08 3.3466335E-08 gauss-seidel spectral radius is 0.9890537 estimated iterations to convergence 78 setup time was (sec) 0.5700000 now iterating at: 05:19:36 rms-change max change #iterations 0.1849981 27.48005 at 10iterations 2.1449994E-02 2.983131 at 20iterations 2.5888362E-03 0.3845940 at 30iterations 3.2958185E-04 4.1625977E-02 at 40iterations 5.5838234E-05 9.1791153E-03 at 50iterations finished qdiffx linear iterations at : 05:19:39 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 5.5838234E-05 9.1791153E-03 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.010000 DelPhi exited at 05:19:40 4.012u 0.281s 0:04.76 90.1% 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 05:19:40 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2305 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: ZN6 650 has a net charge of 1.4000 !!! WARNING: ZN6 651 has a net charge of 1.4000 !!! WARNING: ZN6 652 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.069527 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): 15.69200 63.03500 ymin,ymax (A): -3.547000 33.92600 zmin,zma (A): 20.16900 71.77500 x,y,z range (A): 47.34300 37.47300 51.60600 scale (grids/A): 2.069527 object centre (A): 39.36350 15.18950 45.97200 number of atom coordinates read : 2305 total number of charged atoms : 1983 net assigned charge : 10.40001 assigned positive charge : 325.3839 centred at (gu) : 94.28824 89.02805 87.66094 assigned negative charge : -314.9841 centred at (gu) : 94.57575 88.85036 87.29543 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 72084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17745 grid for indexing accessible points = 1.400000 m= 28667 mr = 51055 m= 5365 mr = 21742 m= 427 mr = 3514 m= 5 mr = 186 m= 0 mr = 2 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 30049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15723 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) : 0.6898422 object centre at (A) : 39.36350 15.18950 45.97200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3123793E-02 5.9038419E-02 midg,1,midg; midg,igrid,midg 2.8068930E-02 4.3832030E-02 1,midg,midg; igrid,midg,midg 2.6321793E-02 2.9150767E-02 gauss-seidel spectral radius is 0.9987803 estimated iterations to convergence 227 setup time was (sec) 0.9700000 now iterating at: 05:19:41 rms-change max change #iterations 4.486737 196.6920 at 10iterations 2.202065 71.45087 at 20iterations 1.069818 34.45024 at 30iterations 0.5239955 19.25181 at 40iterations 0.2562379 8.516152 at 50iterations 0.1257244 3.575167 at 60iterations 6.1306696E-02 1.944359 at 70iterations 3.0016597E-02 0.9088612 at 80iterations 1.4714001E-02 0.4540071 at 90iterations 7.1879579E-03 0.2320876 at 100iterations 3.5217344E-03 0.1047220 at 110iterations 1.7248703E-03 5.5249929E-02 at 120iterations finished qdiffx linear iterations at : 05:19:49 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 1.7248703E-03 5.5249929E-02 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.350000 DelPhi exited at 05:19:50 9.355u 0.296s 0:10.19 94.6% 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 05:19:50 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2305 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: ZN6 650 has a net charge of 1.4000 !!! WARNING: ZN6 651 has a net charge of 1.4000 !!! WARNING: ZN6 652 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.104290 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): 15.69200 63.03500 ymin,ymax (A): -3.547000 33.92600 zmin,zma (A): 20.16900 71.77500 x,y,z range (A): 47.34300 37.47300 51.60600 scale (grids/A): 3.104290 object centre (A): 39.36350 15.18950 45.97200 number of atom coordinates read : 2305 total number of charged atoms : 1983 net assigned charge : 10.40001 assigned positive charge : 325.3839 centred at (gu) : 96.43242 88.54195 86.49138 assigned negative charge : -314.9841 centred at (gu) : 96.86366 88.27568 85.94315 start vw surface at 0.1600000 fill in re-entrant regions at 0.9600000 boundary points on vw surface= 166282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17745 grid for indexing accessible points = 1.400000 m= 89743 mr = 123060 m= 35851 mr = 74647 m= 9942 mr = 29375 m= 1844 mr = 7665 m= 174 mr = 1335 m= 3 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.130000 number of dielectric boundary points 67659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 15864 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) : 2.069527 object centre at (A) : 39.36350 15.18950 45.97200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4522487 0.4679106 midg,1,midg; midg,igrid,midg 0.2560952 0.3944671 1,midg,midg; igrid,midg,midg 0.2162294 0.5140923 gauss-seidel spectral radius is 0.9992845 estimated iterations to convergence 295 setup time was (sec) 2.450000 now iterating at: 05:19:53 rms-change max change #iterations 10.12013 415.0491 at 10iterations 5.959078 176.3724 at 20iterations 3.506528 87.29478 at 30iterations 2.056553 40.43710 at 40iterations 1.204173 23.86810 at 50iterations 0.7051439 14.50867 at 60iterations 0.4117512 7.937498 at 70iterations 0.2404223 4.703838 at 80iterations 0.1402759 2.495014 at 90iterations 8.1658304E-02 1.454649 at 100iterations 4.7684126E-02 0.9489269 at 110iterations 2.7775133E-02 0.5399828 at 120iterations 1.6198782E-02 0.3011780 at 130iterations 9.4541116E-03 0.1809440 at 140iterations 5.5457111E-03 9.6099854E-02 at 150iterations 3.2712070E-03 5.8864594E-02 at 160iterations 1.9543516E-03 3.6224365E-02 at 170iterations 1.1901073E-03 2.1469116E-02 at 180iterations finished qdiffx linear iterations at : 05:20:06 total time elapsed so far: 15.92000 # loops : 180 mean,max change (kT/e) : 1.1901073E-03 2.1469116E-02 energy calculations done at 15.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.09000 DelPhi exited at 05:20:07 16.090u 0.308s 0:16.86 97.2% 0+0k 0+0io 0pf+0w