Sat Oct 8 22:53:47 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 8 2011 at 22:53:47 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 = 2332 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5913622 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): -12.46300 39.34000 ymin,ymax (A): -30.58100 29.61900 zmin,zma (A): -9.596000 32.68100 x,y,z range (A): 51.80300 60.20000 42.27700 scale (grids/A): 0.5913622 object centre (A): 13.43850 -0.4809999 11.54250 number of atom coordinates read : 2332 total number of charged atoms : 2197 net assigned charge : 10.00003 assigned positive charge : 335.2285 centred at (gu) : 89.20878 90.06240 90.99352 assigned negative charge : -325.2291 centred at (gu) : 89.20269 90.13085 90.91009 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5509 nv = 96 ne = 84 npr = 46475 no. pairs analyzed = 46475 no. exposed pairs = 3203 no. arc points = 22681 no. surface atoms = 1065 nbur = 1267 mkacc time = 0.1100000 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= 269 mr = 2712 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2323 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6893 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0112675E-09 6.4258496E-09 midg,1,midg; midg,igrid,midg 4.7124051E-09 1.6128505E-09 1,midg,midg; igrid,midg,midg 3.6462209E-09 2.8021341E-09 gauss-seidel spectral radius is 0.9851917 estimated iterations to convergence 67 setup time was (sec) 0.4900000 now iterating at: 22:53:48 rms-change max change #iterations 9.1085538E-02 14.48344 at 10iterations 7.3606698E-03 1.144279 at 20iterations 5.9601635E-04 0.1041965 at 30iterations 4.8863993E-05 9.3936920E-03 at 40iterations 4.1350463E-06 6.9236755E-04 at 50iterations finished qdiffx linear iterations at : 22:53:50 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 4.1350463E-06 6.9236755E-04 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 22:53:51 3.042u 0.156s 0:03.48 91.6% 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 Sat Oct 8 2011 at 22:53:51 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 = 2332 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.774086 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): -12.46300 39.34000 ymin,ymax (A): -30.58100 29.61900 zmin,zma (A): -9.596000 32.68100 x,y,z range (A): 51.80300 60.20000 42.27700 scale (grids/A): 1.774086 object centre (A): 13.43850 -0.4809999 11.54250 number of atom coordinates read : 2332 total number of charged atoms : 2197 net assigned charge : 10.00003 assigned positive charge : 335.2285 centred at (gu) : 87.62603 90.18688 92.98025 assigned negative charge : -325.2291 centred at (gu) : 87.60805 90.39235 92.73041 start vw surface at 0.2000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 59158 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22681 grid for indexing accessible points = 1.400000 m= 19272 mr = 38392 m= 2532 mr = 13186 m= 93 mr = 1322 m= 0 mr = 9 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.5000000 number of dielectric boundary points 28146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 206 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 17161 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) : 0.5913622 object centre at (A) : 13.43850 -0.4809999 11.54250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6585315E-03 1.7155617E-02 midg,1,midg; midg,igrid,midg 3.5763327E-02 1.3741440E-02 1,midg,midg; igrid,midg,midg 2.5648683E-02 1.4342708E-02 gauss-seidel spectral radius is 0.9984152 estimated iterations to convergence 199 setup time was (sec) 0.7500000 now iterating at: 22:53:52 rms-change max change #iterations 3.367259 155.5058 at 10iterations 1.470662 62.27991 at 20iterations 0.6490324 27.37126 at 30iterations 0.2856182 10.36048 at 40iterations 0.1259845 5.016344 at 50iterations 5.5747271E-02 2.217560 at 60iterations 2.4489447E-02 0.8769112 at 70iterations 1.0842075E-02 0.3939152 at 80iterations 4.7622952E-03 0.1882172 at 90iterations 2.1032421E-03 7.2540283E-02 at 100iterations 9.3010766E-04 3.2604218E-02 at 110iterations 4.1013781E-04 1.5823364E-02 at 120iterations finished qdiffx linear iterations at : 22:53:58 total time elapsed so far: 6.680000 # loops : 120 mean,max change (kT/e) : 4.1013781E-04 1.5823364E-02 energy calculations done at 6.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.860000 DelPhi exited at 22:53:58 6.865u 0.180s 0:07.32 96.1% 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 Sat Oct 8 2011 at 22:53:58 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 = 2332 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.661130 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): -12.46300 39.34000 ymin,ymax (A): -30.58100 29.61900 zmin,zma (A): -9.596000 32.68100 x,y,z range (A): 51.80300 60.20000 42.27700 scale (grids/A): 2.661130 object centre (A): 13.43850 -0.4809999 11.54250 number of atom coordinates read : 2332 total number of charged atoms : 2197 net assigned charge : 10.00003 assigned positive charge : 335.2285 centred at (gu) : 86.43886 90.28021 94.47030 assigned negative charge : -325.2291 centred at (gu) : 86.41211 90.58855 94.09569 start vw surface at 0.1800000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 136915 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22681 grid for indexing accessible points = 1.400000 m= 63544 mr = 93975 m= 20769 mr = 49539 m= 4244 mr = 15823 m= 403 mr = 2850 m= 9 mr = 200 m= 0 mr = 0 time to grow re-entrant surface = 0.5699999 no. cavity mid-points inaccessible to solvent = 242 time to turn everything in is 1.050000 number of dielectric boundary points 63497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 17573 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) : 1.774086 object centre at (A) : 13.43850 -0.4809999 11.54250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3560127E-02 0.1959386 midg,1,midg; midg,igrid,midg 0.6294479 0.3007187 1,midg,midg; igrid,midg,midg 0.2701309 0.1589598 gauss-seidel spectral radius is 0.9992022 estimated iterations to convergence 280 setup time was (sec) 1.330000 now iterating at: 22:54:00 rms-change max change #iterations 8.290481 330.2405 at 10iterations 4.781206 133.4849 at 20iterations 2.738582 78.00878 at 30iterations 1.558080 35.59393 at 40iterations 0.8840299 19.77303 at 50iterations 0.5017329 11.12712 at 60iterations 0.2829474 6.357322 at 70iterations 0.1601454 3.545409 at 80iterations 9.0124182E-02 1.863223 at 90iterations 5.0849017E-02 1.038866 at 100iterations 2.8589001E-02 0.6093092 at 110iterations 1.6053826E-02 0.3337111 at 120iterations 9.0483679E-03 0.1834469 at 130iterations 5.0798245E-03 0.1110306 at 140iterations 2.8542839E-03 6.1851501E-02 at 150iterations 1.6063708E-03 4.0741622E-02 at 160iterations 9.0139260E-04 1.9043446E-02 at 170iterations 5.0761318E-04 1.1102676E-02 at 180iterations finished qdiffx linear iterations at : 22:54:09 total time elapsed so far: 10.58000 # loops : 180 mean,max change (kT/e) : 5.0761318E-04 1.1102676E-02 energy calculations done at 10.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.76000 DelPhi exited at 22:54:09 10.765u 0.151s 0:11.20 97.4% 0+0k 0+0io 0pf+0w