Sat Oct 15 12:24:57 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 Sat Oct 15 2011 at 12:24:57 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2342 !!! WARNING: HIR 82 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6486880 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): -14.93300 39.94700 ymin,ymax (A): -19.26100 25.46700 zmin,zma (A): -5.320000 48.46300 x,y,z range (A): 54.88000 44.72800 53.78300 scale (grids/A): 0.6486880 object centre (A): 12.50700 3.103000 21.57150 number of atom coordinates read : 2342 total number of charged atoms : 2208 net assigned charge : -3.986000 assigned positive charge : 309.4745 centred at (gu) : 91.67982 90.13751 89.88123 assigned negative charge : -313.4610 centred at (gu) : 91.59537 90.17020 90.11741 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7228 nv = 96 ne = 84 npr = 47586 no. pairs analyzed = 47586 no. exposed pairs = 3321 no. arc points = 24910 no. surface atoms = 1108 nbur = 1234 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 493 mr = 3520 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 4153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2071 ## 119 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8025 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0276252E-08 -3.5435949E-08 midg,1,midg; midg,igrid,midg -3.6177008E-09 -1.1809650E-08 1,midg,midg; igrid,midg,midg -1.2465653E-08 3.6051730E-09 gauss-seidel spectral radius is 0.9876894 estimated iterations to convergence 74 setup time was (sec) 0.3800000 now iterating at: 12:24:57 rms-change max change #iterations 0.1414500 21.69118 at 10iterations 1.4247771E-02 2.097458 at 20iterations 1.5062686E-03 0.2254219 at 30iterations 2.0955125E-04 2.5890350E-02 at 40iterations 5.0283856E-05 6.6876411E-03 at 50iterations finished qdiffx linear iterations at : 12:25:00 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 5.0283856E-05 6.6876411E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 12:25:01 3.474u 0.197s 0:03.93 93.1% 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 15 2011 at 12:25:01 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2342 !!! WARNING: HIR 82 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.946064 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): -14.93300 39.94700 ymin,ymax (A): -19.26100 25.46700 zmin,zma (A): -5.320000 48.46300 x,y,z range (A): 54.88000 44.72800 53.78300 scale (grids/A): 1.946064 object centre (A): 12.50700 3.103000 21.57150 number of atom coordinates read : 2342 total number of charged atoms : 2208 net assigned charge : -3.986000 assigned positive charge : 309.4745 centred at (gu) : 95.03902 90.41221 89.64363 assigned negative charge : -313.4610 centred at (gu) : 94.78619 90.51056 90.35227 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 75926 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24910 grid for indexing accessible points = 1.400000 m= 27770 mr = 49235 m= 5484 mr = 18772 m= 419 mr = 3171 m= 8 mr = 150 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 0.3800000 number of dielectric boundary points 38279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 17469 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) : 0.6486880 object centre at (A) : 12.50700 3.103000 21.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4450056E-02 -5.7046238E-02 midg,1,midg; midg,igrid,midg 4.4997111E-03 3.3859380E-03 1,midg,midg; igrid,midg,midg -6.4126952E-03 4.0792879E-03 gauss-seidel spectral radius is 0.9987062 estimated iterations to convergence 220 setup time was (sec) 0.6100000 now iterating at: 12:25:02 rms-change max change #iterations 3.989705 196.7627 at 10iterations 1.921187 66.73798 at 20iterations 0.9143500 33.45141 at 30iterations 0.4391418 14.88706 at 40iterations 0.2090536 6.120707 at 50iterations 0.1005247 3.507004 at 60iterations 4.8078340E-02 1.692668 at 70iterations 2.2954889E-02 0.7740555 at 80iterations 1.0978322E-02 0.3691387 at 90iterations 5.2541783E-03 0.1619446 at 100iterations 2.5245561E-03 8.0632210E-02 at 110iterations 1.2090780E-03 3.6975861E-02 at 120iterations finished qdiffx linear iterations at : 12:25:09 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 1.2090780E-03 3.6975861E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 12:25:10 8.147u 0.218s 0:08.86 94.2% 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 Sat Oct 15 2011 at 12:25:10 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2342 !!! WARNING: HIR 82 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.919096 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): -14.93300 39.94700 ymin,ymax (A): -19.26100 25.46700 zmin,zma (A): -5.320000 48.46300 x,y,z range (A): 54.88000 44.72800 53.78300 scale (grids/A): 2.919096 object centre (A): 12.50700 3.103000 21.57150 number of atom coordinates read : 2342 total number of charged atoms : 2208 net assigned charge : -3.986000 assigned positive charge : 309.4745 centred at (gu) : 97.55830 90.61839 89.46539 assigned negative charge : -313.4610 centred at (gu) : 97.17926 90.76567 90.52838 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 175579 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24910 grid for indexing accessible points = 1.400000 m= 86019 mr = 120624 m= 34484 mr = 66697 m= 9780 mr = 26006 m= 1656 mr = 6923 m= 122 mr = 1026 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.000000 number of dielectric boundary points 86315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 17664 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) : 1.946064 object centre at (A) : 12.50700 3.103000 21.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1126697 -0.4418740 midg,1,midg; midg,igrid,midg 2.6645210E-02 5.7211511E-02 1,midg,midg; igrid,midg,midg -3.9583605E-02 6.1999723E-02 gauss-seidel spectral radius is 0.9993058 estimated iterations to convergence 299 setup time was (sec) 1.240000 now iterating at: 12:25:11 rms-change max change #iterations 9.471394 336.1355 at 10iterations 5.679788 127.1131 at 20iterations 3.392192 72.82085 at 30iterations 2.013207 43.09143 at 40iterations 1.191345 25.36246 at 50iterations 0.7040893 14.60052 at 60iterations 0.4147642 7.438263 at 70iterations 0.2440891 4.921200 at 80iterations 0.1434749 2.753078 at 90iterations 8.4305227E-02 1.585938 at 100iterations 4.9361996E-02 0.9665031 at 110iterations 2.8966906E-02 0.5227222 at 120iterations 1.6964151E-02 0.2981367 at 130iterations 9.9322218E-03 0.1708069 at 140iterations 5.8250846E-03 0.1122904 at 150iterations 3.4208663E-03 6.2511921E-02 at 160iterations 2.0022204E-03 3.5417080E-02 at 170iterations 1.1754909E-03 2.0866394E-02 at 180iterations finished qdiffx linear iterations at : 12:25:23 total time elapsed so far: 13.11000 # loops : 180 mean,max change (kT/e) : 1.1754909E-03 2.0866394E-02 energy calculations done at 13.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 12:25:24 13.263u 0.239s 0:13.90 97.0% 0+0k 0+0io 0pf+0w