Tue Oct 11 08:35:43 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 Tue Oct 11 2011 at 08:35:43 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.6475199 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): -1.292000 53.68700 ymin,ymax (A): -22.73600 22.22700 zmin,zma (A): 9.145000 54.58700 x,y,z range (A): 54.97900 44.96300 45.44200 scale (grids/A): 0.6475199 object centre (A): 26.19750 -0.2545004 31.86600 number of atom coordinates read : 2380 total number of charged atoms : 2242 net assigned charge : 5.025008 assigned positive charge : 358.3923 centred at (gu) : 88.56494 90.54905 90.14023 assigned negative charge : -353.3678 centred at (gu) : 88.57931 90.49622 89.95776 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6798 nv = 96 ne = 84 npr = 47878 no. pairs analyzed = 47878 no. exposed pairs = 2852 no. arc points = 20211 no. surface atoms = 975 nbur = 1405 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 3840 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1964 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7857 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4734378E-08 3.3148638E-08 midg,1,midg; midg,igrid,midg 1.8794695E-09 1.7697529E-08 1,midg,midg; igrid,midg,midg 1.4574987E-08 5.3227427E-09 gauss-seidel spectral radius is 0.9876206 estimated iterations to convergence 73 setup time was (sec) 0.6000000 now iterating at: 08:35:44 rms-change max change #iterations 0.1475362 26.85035 at 10iterations 1.5470853E-02 2.252118 at 20iterations 1.7157164E-03 0.2261658 at 30iterations 2.0496007E-04 3.9695740E-02 at 40iterations 2.9148932E-05 4.2762756E-03 at 50iterations finished qdiffx linear iterations at : 08:35:48 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 2.9148932E-05 4.2762756E-03 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 08:35:48 4.116u 0.266s 0:04.95 88.2% 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 Tue Oct 11 2011 at 08:35:48 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 1.942560 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): -1.292000 53.68700 ymin,ymax (A): -22.73600 22.22700 zmin,zma (A): 9.145000 54.58700 x,y,z range (A): 54.97900 44.96300 45.44200 scale (grids/A): 1.942560 object centre (A): 26.19750 -0.2545004 31.86600 number of atom coordinates read : 2380 total number of charged atoms : 2242 net assigned charge : 5.025008 assigned positive charge : 358.3923 centred at (gu) : 85.69420 91.64694 90.42047 assigned negative charge : -353.3678 centred at (gu) : 85.73798 91.48876 89.87318 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 72639 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20211 grid for indexing accessible points = 1.400000 m= 27959 mr = 51028 m= 4444 mr = 21286 m= 280 mr = 2789 m= 1 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 30113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 17640 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) : 0.6475199 object centre at (A) : 26.19750 -0.2545004 31.86600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1124430E-02 4.3654907E-02 midg,1,midg; midg,igrid,midg -2.0232068E-03 6.7502698E-03 1,midg,midg; igrid,midg,midg 2.6927546E-02 2.6059479E-02 gauss-seidel spectral radius is 0.9986645 estimated iterations to convergence 217 setup time was (sec) 0.9600000 now iterating at: 08:35:50 rms-change max change #iterations 4.200385 184.9451 at 10iterations 1.984552 73.13178 at 20iterations 0.9402241 30.10245 at 30iterations 0.4465312 13.83123 at 40iterations 0.2113998 7.158436 at 50iterations 9.9799477E-02 3.254622 at 60iterations 4.7191214E-02 1.776767 at 70iterations 2.2366891E-02 0.7393698 at 80iterations 1.0627988E-02 0.3419952 at 90iterations 5.0184350E-03 0.1543427 at 100iterations 2.3992725E-03 7.8567505E-02 at 110iterations 1.1387586E-03 3.6470413E-02 at 120iterations finished qdiffx linear iterations at : 08:35:58 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 1.1387586E-03 3.6470413E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.560000 DelPhi exited at 08:35:59 9.564u 0.297s 0:10.44 94.3% 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 08:35:59 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.913840 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): -1.292000 53.68700 ymin,ymax (A): -22.73600 22.22700 zmin,zma (A): 9.145000 54.58700 x,y,z range (A): 54.97900 44.96300 45.44200 scale (grids/A): 2.913840 object centre (A): 26.19750 -0.2545004 31.86600 number of atom coordinates read : 2380 total number of charged atoms : 2242 net assigned charge : 5.025008 assigned positive charge : 358.3923 centred at (gu) : 83.54116 92.47038 90.63062 assigned negative charge : -353.3678 centred at (gu) : 83.60691 92.23304 89.80984 start vw surface at 0.1600000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 167384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20211 grid for indexing accessible points = 1.400000 m= 89250 mr = 122975 m= 33964 mr = 74409 m= 8087 mr = 27857 m= 1148 mr = 5972 m= 75 mr = 792 m= 0 mr = 36 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.710000 number of dielectric boundary points 67867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 17933 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) : 1.942560 object centre at (A) : 26.19750 -0.2545004 31.86600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2825478 0.4665513 midg,1,midg; midg,igrid,midg -2.9761564E-02 -1.6333085E-02 1,midg,midg; igrid,midg,midg 0.1842648 0.1586227 gauss-seidel spectral radius is 0.9992589 estimated iterations to convergence 290 setup time was (sec) 2.050000 now iterating at: 08:36:01 rms-change max change #iterations 9.820453 498.3674 at 10iterations 5.735646 134.7836 at 20iterations 3.338945 93.78811 at 30iterations 1.937422 43.94167 at 40iterations 1.118860 28.06511 at 50iterations 0.6469761 14.76315 at 60iterations 0.3734814 8.237018 at 70iterations 0.2157118 4.485540 at 80iterations 0.1239737 2.373550 at 90iterations 7.1473897E-02 1.319652 at 100iterations 4.1101180E-02 0.7325597 at 110iterations 2.3688994E-02 0.4290915 at 120iterations 1.3660294E-02 0.2719007 at 130iterations 7.8651756E-03 0.1412888 at 140iterations 4.5383372E-03 7.8550339E-02 at 150iterations 2.6308922E-03 4.7706604E-02 at 160iterations 1.5370990E-03 3.1316757E-02 at 170iterations 9.0643397E-04 1.7009735E-02 at 180iterations finished qdiffx linear iterations at : 08:36:15 total time elapsed so far: 15.84000 # loops : 180 mean,max change (kT/e) : 9.0643397E-04 1.7009735E-02 energy calculations done at 15.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.02000 DelPhi exited at 08:36:16 16.019u 0.308s 0:16.87 96.6% 0+0k 0+0io 0pf+0w