Mon Oct 10 17:11:12 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 Mon Oct 10 2011 at 17:11:12 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1838 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: 0.6999469 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): -27.22700 23.63400 ymin,ymax (A): -2.674000 38.09800 zmin,zma (A): 26.24700 76.41900 x,y,z range (A): 50.86100 40.77200 50.17200 scale (grids/A): 0.6999469 object centre (A): -1.796500 17.71200 51.33300 number of atom coordinates read : 1838 total number of charged atoms : 1708 net assigned charge : -6.999988 assigned positive charge : 261.4214 centred at (gu) : 88.41885 90.16698 91.12144 assigned negative charge : -268.4212 centred at (gu) : 88.47281 90.28841 91.24799 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6177 nv = 96 ne = 84 npr = 38444 no. pairs analyzed = 38444 no. exposed pairs = 2360 no. arc points = 17331 no. surface atoms = 793 nbur = 1045 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 347 mr = 3240 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 94 time to turn everything in is 0.2500000 number of dielectric boundary points 3226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1466 ## 109 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6763 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7950278E-09 -1.1809372E-07 midg,1,midg; midg,igrid,midg -5.7886549E-09 -9.5901562E-08 1,midg,midg; igrid,midg,midg -3.9585490E-08 -5.0432057E-08 gauss-seidel spectral radius is 0.9893513 estimated iterations to convergence 79 setup time was (sec) 0.5700000 now iterating at: 17:11:13 rms-change max change #iterations 0.1846607 30.90672 at 10iterations 2.1642556E-02 3.207464 at 20iterations 2.5802108E-03 0.3501253 at 30iterations 3.1286755E-04 4.8919678E-02 at 40iterations 3.7489463E-05 5.9280396E-03 at 50iterations finished qdiffx linear iterations at : 17:11:18 total time elapsed so far: 4.770000 # loops : 50 mean,max change (kT/e) : 3.7489463E-05 5.9280396E-03 energy calculations done at 4.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.930000 DelPhi exited at 17:11:18 4.932u 0.459s 0:05.69 94.5% 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 17:11:18 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1838 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: 2.099841 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): -27.22700 23.63400 ymin,ymax (A): -2.674000 38.09800 zmin,zma (A): 26.24700 76.41900 x,y,z range (A): 50.86100 40.77200 50.17200 scale (grids/A): 2.099841 object centre (A): -1.796500 17.71200 51.33300 number of atom coordinates read : 1838 total number of charged atoms : 1708 net assigned charge : -6.999988 assigned positive charge : 261.4214 centred at (gu) : 85.25674 90.50132 93.36462 assigned negative charge : -268.4212 centred at (gu) : 85.41866 90.86531 93.74400 start vw surface at 0.1000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 65893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17331 grid for indexing accessible points = 1.400000 m= 23244 mr = 44110 m= 4007 mr = 16743 m= 305 mr = 2503 m= 9 mr = 139 m= 0 mr = 4 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 2091 time to turn everything in is 0.5500000 number of dielectric boundary points 29959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 13558 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) : 0.6999469 object centre at (A) : -1.796500 17.71200 51.33300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5776195E-02 -9.0235792E-02 midg,1,midg; midg,igrid,midg -2.2360752E-04 -2.0788508E-02 1,midg,midg; igrid,midg,midg 2.2743411E-02 5.3678928E-03 gauss-seidel spectral radius is 0.9988023 estimated iterations to convergence 229 setup time was (sec) 0.8700000 now iterating at: 17:11:20 rms-change max change #iterations 4.184356 183.0505 at 10iterations 2.041269 72.94505 at 20iterations 0.9979505 33.74876 at 30iterations 0.4900582 15.17135 at 40iterations 0.2411144 7.750021 at 50iterations 0.1177948 3.926327 at 60iterations 5.7837784E-02 1.887373 at 70iterations 2.8396282E-02 0.9202881 at 80iterations 1.3914451E-02 0.4358063 at 90iterations 6.8327039E-03 0.2142000 at 100iterations 3.3517818E-03 0.1016693 at 110iterations 1.6438102E-03 4.9179077E-02 at 120iterations finished qdiffx linear iterations at : 17:11:30 total time elapsed so far: 11.64000 # loops : 120 mean,max change (kT/e) : 1.6438102E-03 4.9179077E-02 energy calculations done at 11.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 17:11:31 11.811u 0.513s 0:12.96 95.0% 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 17:11:31 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1838 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: 3.149761 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): -27.22700 23.63400 ymin,ymax (A): -2.674000 38.09800 zmin,zma (A): 26.24700 76.41900 x,y,z range (A): 50.86100 40.77200 50.17200 scale (grids/A): 3.149761 object centre (A): -1.796500 17.71200 51.33300 number of atom coordinates read : 1838 total number of charged atoms : 1708 net assigned charge : -6.999988 assigned positive charge : 261.4214 centred at (gu) : 82.88515 90.75200 95.04694 assigned negative charge : -268.4212 centred at (gu) : 83.12802 91.29803 95.61599 start vw surface at 0.1000000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 151954 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17331 grid for indexing accessible points = 1.400000 m= 74121 mr = 106696 m= 27584 mr = 59826 m= 7349 mr = 22001 m= 1280 mr = 5478 m= 127 mr = 906 m= 3 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 7193 time to turn everything in is 1.920000 number of dielectric boundary points 67428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 13664 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) : 2.099841 object centre at (A) : -1.796500 17.71200 51.33300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9698486 -0.7753056 midg,1,midg; midg,igrid,midg 1.5070754E-02 -0.1362593 1,midg,midg; igrid,midg,midg 0.1145006 0.1730738 gauss-seidel spectral radius is 0.9992975 estimated iterations to convergence 298 setup time was (sec) 2.290000 now iterating at: 17:11:34 rms-change max change #iterations 9.367539 362.9849 at 10iterations 5.504640 130.2187 at 20iterations 3.231426 77.54357 at 30iterations 1.894905 38.26009 at 40iterations 1.108545 21.95042 at 50iterations 0.6494338 13.02427 at 60iterations 0.3778854 7.021823 at 70iterations 0.2209691 4.328308 at 80iterations 0.1285084 2.334610 at 90iterations 7.5001225E-02 1.392370 at 100iterations 4.3764096E-02 0.8287506 at 110iterations 2.5528153E-02 0.5161273 at 120iterations 1.4846412E-02 0.2891607 at 130iterations 8.6369272E-03 0.1538196 at 140iterations 5.0304146E-03 9.5325470E-02 at 150iterations 2.9386156E-03 5.2101135E-02 at 160iterations 1.7102994E-03 2.9598236E-02 at 170iterations 9.9500385E-04 1.7587900E-02 at 180iterations finished qdiffx linear iterations at : 17:11:52 total time elapsed so far: 20.08000 # loops : 180 mean,max change (kT/e) : 9.9500385E-04 1.7587900E-02 energy calculations done at 20.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.25000 DelPhi exited at 17:11:52 20.257u 0.527s 0:21.12 98.3% 0+0k 0+0io 0pf+0w