Mon Oct 10 17:01:48 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 17:01:49 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: 246 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2989 !!! WARNING: WAT 5 has a net charge of -0.8340 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: 0.6062980 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): 13.43500 71.38200 ymin,ymax (A): 3.795000 50.90300 zmin,zma (A): 7.536000 66.25300 x,y,z range (A): 57.94701 47.10800 58.71700 scale (grids/A): 0.6062980 object centre (A): 42.40850 27.34900 36.89450 number of atom coordinates read : 2989 total number of charged atoms : 2838 net assigned charge : -4.333964 assigned positive charge : 446.8829 centred at (gu) : 89.28976 90.38578 90.45405 assigned negative charge : -451.2181 centred at (gu) : 89.14961 90.49120 90.58051 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7317 nv = 96 ne = 84 npr = 59883 no. pairs analyzed = 59883 no. exposed pairs = 3870 no. arc points = 27516 no. surface atoms = 1309 nbur = 1680 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3822 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2759 ## 294 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9069 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8323509E-09 -9.6934247E-09 midg,1,midg; midg,igrid,midg 2.9289109E-09 -8.3293914E-09 1,midg,midg; igrid,midg,midg -1.1130970E-08 4.1904573E-09 gauss-seidel spectral radius is 0.9859571 estimated iterations to convergence 69 setup time was (sec) 0.4200000 now iterating at: 17:01:49 rms-change max change #iterations 0.1207316 17.18600 at 10iterations 1.0642705E-02 1.431379 at 20iterations 9.3412033E-04 0.1569595 at 30iterations 8.1705060E-05 1.1871338E-02 at 40iterations 7.2853027E-06 9.6321106E-04 at 50iterations finished qdiffx linear iterations at : 17:01:52 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 7.2853027E-06 9.6321106E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 17:01:53 3.481u 0.162s 0:04.57 79.6% 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 Mon Oct 10 2011 at 17:01:53 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: 246 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2989 !!! WARNING: WAT 5 has a net charge of -0.8340 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: 1.818894 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): 13.43500 71.38200 ymin,ymax (A): 3.795000 50.90300 zmin,zma (A): 7.536000 66.25300 x,y,z range (A): 57.94701 47.10800 58.71700 scale (grids/A): 1.818894 object centre (A): 42.40850 27.34900 36.89450 number of atom coordinates read : 2989 total number of charged atoms : 2838 net assigned charge : -4.333964 assigned positive charge : 446.8829 centred at (gu) : 87.86849 91.15643 91.36127 assigned negative charge : -451.2181 centred at (gu) : 87.44848 91.47311 91.74119 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27516 grid for indexing accessible points = 1.400000 m= 26161 mr = 53842 m= 3256 mr = 18431 m= 135 mr = 1759 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 660 time to turn everything in is 0.4100000 number of dielectric boundary points 35301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 22204 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) : 0.6062980 object centre at (A) : 42.40850 27.34900 36.89450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4665170E-02 -5.3245487E-04 midg,1,midg; midg,igrid,midg 9.9852402E-04 -2.7348168E-02 1,midg,midg; igrid,midg,midg -4.2746313E-02 2.8814211E-02 gauss-seidel spectral radius is 0.9985522 estimated iterations to convergence 208 setup time was (sec) 0.6700000 now iterating at: 17:01:54 rms-change max change #iterations 4.211077 191.0043 at 10iterations 1.920850 68.69887 at 20iterations 0.8743863 27.83823 at 30iterations 0.4000478 14.10821 at 40iterations 0.1831256 6.123302 at 50iterations 8.3485171E-02 2.675771 at 60iterations 3.8087782E-02 1.259609 at 70iterations 1.7457377E-02 0.5434639 at 80iterations 7.9994584E-03 0.2617426 at 90iterations 3.6749062E-03 0.1204705 at 100iterations 1.6756217E-03 4.8925400E-02 at 110iterations 7.6882681E-04 2.6633620E-02 at 120iterations finished qdiffx linear iterations at : 17:02:02 total time elapsed so far: 8.740000 # loops : 120 mean,max change (kT/e) : 7.6882681E-04 2.6633620E-02 energy calculations done at 8.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.870000 DelPhi exited at 17:02:03 8.876u 0.267s 0:09.88 92.4% 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 Mon Oct 10 2011 at 17:02:03 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: 246 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2989 !!! WARNING: WAT 5 has a net charge of -0.8340 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: 2.728341 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): 13.43500 71.38200 ymin,ymax (A): 3.795000 50.90300 zmin,zma (A): 7.536000 66.25300 x,y,z range (A): 57.94701 47.10800 58.71700 scale (grids/A): 2.728341 object centre (A): 42.40850 27.34900 36.89450 number of atom coordinates read : 2989 total number of charged atoms : 2838 net assigned charge : -4.333964 assigned positive charge : 446.8829 centred at (gu) : 86.80266 91.73431 92.04175 assigned negative charge : -451.2181 centred at (gu) : 86.17262 92.20959 92.61169 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 184480 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27516 grid for indexing accessible points = 1.400000 m= 87654 mr = 130947 m= 28079 mr = 69996 m= 5399 mr = 21545 m= 573 mr = 3710 m= 29 mr = 361 m= 0 mr = 9 time to grow re-entrant surface = 0.5799999 no. cavity mid-points inaccessible to solvent = 2214 time to turn everything in is 1.070000 number of dielectric boundary points 79646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 22699 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) : 1.818894 object centre at (A) : 42.40850 27.34900 36.89450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1760714 0.1972206 midg,1,midg; midg,igrid,midg -1.5321291E-03 -0.2583739 1,midg,midg; igrid,midg,midg -0.4754866 0.4372013 gauss-seidel spectral radius is 0.9992555 estimated iterations to convergence 289 setup time was (sec) 1.360000 now iterating at: 17:02:05 rms-change max change #iterations 10.16837 315.6460 at 10iterations 5.975075 156.5262 at 20iterations 3.481175 78.12663 at 30iterations 2.015055 43.33837 at 40iterations 1.165326 26.50449 at 50iterations 0.6730933 13.64744 at 60iterations 0.3886643 7.618834 at 70iterations 0.2238897 3.948694 at 80iterations 0.1283970 2.446297 at 90iterations 7.3940985E-02 1.369755 at 100iterations 4.2443331E-02 0.8161273 at 110iterations 2.4364430E-02 0.4430695 at 120iterations 1.3988487E-02 0.2490883 at 130iterations 8.0230078E-03 0.1494617 at 140iterations 4.6080197E-03 8.5191727E-02 at 150iterations 2.6393468E-03 5.0949097E-02 at 160iterations 1.5174955E-03 2.6115656E-02 at 170iterations 8.6941849E-04 1.6521454E-02 at 180iterations finished qdiffx linear iterations at : 17:02:18 total time elapsed so far: 14.40000 # loops : 180 mean,max change (kT/e) : 8.6941849E-04 1.6521454E-02 energy calculations done at 14.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.53000 DelPhi exited at 17:02:19 14.534u 0.321s 0:15.40 96.4% 0+0k 0+0io 0pf+0w