Sat Oct 15 12:58:20 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 15 2011 at 12:58:20 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 = 2360 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: 0.7013673 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): -1.193000 46.02000 ymin,ymax (A): 36.18900 86.94700 zmin,zma (A): -24.38100 25.11500 x,y,z range (A): 47.21300 50.75800 49.49600 scale (grids/A): 0.7013673 object centre (A): 22.41350 61.56800 0.3669996 number of atom coordinates read : 2360 total number of charged atoms : 2219 net assigned charge : 3.500020 assigned positive charge : 358.9691 centred at (gu) : 90.10091 90.03448 91.53796 assigned negative charge : -355.4696 centred at (gu) : 90.23826 90.12898 91.46091 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8080 nv = 96 ne = 84 npr = 46652 no. pairs analyzed = 46652 no. exposed pairs = 3094 no. arc points = 21453 no. surface atoms = 1040 nbur = 1320 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 551 mr = 4458 m= 4 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 4083 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1951 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8798 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2660049E-09 8.4822233E-08 midg,1,midg; midg,igrid,midg 7.0457141E-08 -2.1930605E-08 1,midg,midg; igrid,midg,midg 8.9662571E-08 -4.4201595E-08 gauss-seidel spectral radius is 0.9894399 estimated iterations to convergence 79 setup time was (sec) 0.4000000 now iterating at: 12:58:21 rms-change max change #iterations 0.2074548 26.35410 at 10iterations 2.5194647E-02 3.140266 at 20iterations 3.6258139E-03 0.4584827 at 30iterations 8.1490749E-04 0.1279945 at 40iterations 2.6881605E-04 3.9386749E-02 at 50iterations finished qdiffx linear iterations at : 12:58:24 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 2.6881605E-04 3.9386749E-02 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 12:58:24 3.781u 0.232s 0:04.46 89.9% 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 12:58:24 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 = 2360 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: 2.104102 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): -1.193000 46.02000 ymin,ymax (A): 36.18900 86.94700 zmin,zma (A): -24.38100 25.11500 x,y,z range (A): 47.21300 50.75800 49.49600 scale (grids/A): 2.104102 object centre (A): 22.41350 61.56800 0.3669996 number of atom coordinates read : 2360 total number of charged atoms : 2219 net assigned charge : 3.500020 assigned positive charge : 358.9691 centred at (gu) : 90.30244 90.10309 94.61362 assigned negative charge : -355.4696 centred at (gu) : 90.71455 90.38666 94.38220 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85043 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21453 grid for indexing accessible points = 1.400000 m= 34440 mr = 58843 m= 6510 mr = 25791 m= 559 mr = 4200 m= 12 mr = 281 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 37449 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 17604 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) : 0.7013673 object centre at (A) : 22.41350 61.56800 0.3669996 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0439103E-02 2.9213127E-02 midg,1,midg; midg,igrid,midg 9.5536187E-02 2.2809948E-03 1,midg,midg; igrid,midg,midg -1.4414957E-03 -1.4839336E-02 gauss-seidel spectral radius is 0.9988534 estimated iterations to convergence 234 setup time was (sec) 0.6600000 now iterating at: 12:58:26 rms-change max change #iterations 4.906941 229.8909 at 10iterations 2.432462 80.15341 at 20iterations 1.212405 37.66293 at 30iterations 0.6061316 17.64820 at 40iterations 0.3039529 9.178126 at 50iterations 0.1521121 4.602783 at 60iterations 7.5777426E-02 2.246048 at 70iterations 3.7908521E-02 1.092915 at 80iterations 1.9127181E-02 0.5566578 at 90iterations 9.6768402E-03 0.2888317 at 100iterations 4.9763154E-03 0.1617677 at 110iterations 2.6332187E-03 7.8747988E-02 at 120iterations finished qdiffx linear iterations at : 12:58:36 total time elapsed so far: 8.360000 # loops : 120 mean,max change (kT/e) : 2.6332187E-03 7.8747988E-02 energy calculations done at 8.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.490000 DelPhi exited at 12:58:36 8.489u 0.252s 0:11.88 73.4% 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 Sat Oct 15 2011 at 12:58:36 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 = 2360 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: 3.156153 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): -1.193000 46.02000 ymin,ymax (A): 36.18900 86.94700 zmin,zma (A): -24.38100 25.11500 x,y,z range (A): 47.21300 50.75800 49.49600 scale (grids/A): 3.156153 object centre (A): 22.41350 61.56800 0.3669996 number of atom coordinates read : 2360 total number of charged atoms : 2219 net assigned charge : 3.500020 assigned positive charge : 358.9691 centred at (gu) : 90.45356 90.15443 96.92037 assigned negative charge : -355.4696 centred at (gu) : 91.07181 90.57993 96.57324 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 195738 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21453 grid for indexing accessible points = 1.400000 m= 106782 mr = 142032 m= 43529 mr = 87656 m= 12085 mr = 35607 m= 2256 mr = 9129 m= 235 mr = 1619 m= 13 mr = 156 m= 0 mr = 8 time to grow re-entrant surface = 0.6999999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.340000 number of dielectric boundary points 84431 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 17750 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) : 2.104102 object centre at (A) : 22.41350 61.56800 0.3669996 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2678355 0.4025520 midg,1,midg; midg,igrid,midg 1.404005 -8.9897059E-02 1,midg,midg; igrid,midg,midg -4.5565348E-02 -0.1212298 gauss-seidel spectral radius is 0.9993109 estimated iterations to convergence 301 setup time was (sec) 1.600000 now iterating at: 12:58:38 rms-change max change #iterations 11.09199 424.8685 at 10iterations 6.643866 180.3610 at 20iterations 3.965123 90.82283 at 30iterations 2.362741 43.43722 at 40iterations 1.402835 24.36999 at 50iterations 0.8334522 14.75013 at 60iterations 0.4920713 7.979084 at 70iterations 0.2909260 5.429782 at 80iterations 0.1718592 3.106762 at 90iterations 0.1014395 1.801418 at 100iterations 5.9982061E-02 0.9957047 at 110iterations 3.5517063E-02 0.6046944 at 120iterations 2.1147080E-02 0.3943214 at 130iterations 1.2754433E-02 0.2593842 at 140iterations 7.8547131E-03 0.1513901 at 150iterations 5.0246934E-03 0.1023407 at 160iterations 3.3899965E-03 7.6557159E-02 at 170iterations 2.4335422E-03 5.0022125E-02 at 180iterations finished qdiffx linear iterations at : 12:58:52 total time elapsed so far: 14.70000 # loops : 180 mean,max change (kT/e) : 2.4335422E-03 5.0022125E-02 energy calculations done at 14.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.84000 DelPhi exited at 12:58:52 14.840u 0.262s 0:16.01 94.3% 0+0k 0+0io 0pf+0w