Sun Oct 9 00:06:03 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 Sun Oct 9 2011 at 00:06:03 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 = 2407 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: 0.6402763 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): -26.98100 26.66900 ymin,ymax (A): 8.019000 51.32700 zmin,zma (A): -12.11000 43.49100 x,y,z range (A): 53.65000 43.30800 55.60100 scale (grids/A): 0.6402763 object centre (A): -0.1559992 29.67300 15.69050 number of atom coordinates read : 2407 total number of charged atoms : 2272 net assigned charge : 10.50003 assigned positive charge : 350.1793 centred at (gu) : 90.60271 90.40835 90.75964 assigned negative charge : -339.6801 centred at (gu) : 90.63762 90.34248 90.81430 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6802 nv = 96 ne = 84 npr = 47522 no. pairs analyzed = 47522 no. exposed pairs = 3235 no. arc points = 23171 no. surface atoms = 1076 nbur = 1331 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 402 mr = 3492 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.1800000 number of dielectric boundary points 3659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2338 ## 239 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8075 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7945380E-08 1.1397903E-08 midg,1,midg; midg,igrid,midg 7.9559808E-09 2.4153573E-08 1,midg,midg; igrid,midg,midg 1.6776790E-08 1.3383719E-08 gauss-seidel spectral radius is 0.9873562 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 00:06:04 rms-change max change #iterations 0.1330804 21.25932 at 10iterations 1.2994159E-02 2.228351 at 20iterations 1.2845083E-03 0.1743011 at 30iterations 1.2874215E-04 1.7604828E-02 at 40iterations 1.3411142E-05 2.0828247E-03 at 50iterations finished qdiffx linear iterations at : 00:06:07 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 1.3411142E-05 2.0828247E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 00:06:07 3.512u 0.186s 0:03.95 93.4% 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 Sun Oct 9 2011 at 00:06:07 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 = 2407 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: 1.920829 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): -26.98100 26.66900 ymin,ymax (A): 8.019000 51.32700 zmin,zma (A): -12.11000 43.49100 x,y,z range (A): 53.65000 43.30800 55.60100 scale (grids/A): 1.920829 object centre (A): -0.1559992 29.67300 15.69050 number of atom coordinates read : 2407 total number of charged atoms : 2272 net assigned charge : 10.50003 assigned positive charge : 350.1793 centred at (gu) : 91.80769 91.22493 92.27869 assigned negative charge : -339.6801 centred at (gu) : 91.91290 91.02740 92.44283 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73112 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23171 grid for indexing accessible points = 1.400000 m= 25605 mr = 48720 m= 4143 mr = 18137 m= 275 mr = 2461 m= 1 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2119 time to turn everything in is 0.3700000 number of dielectric boundary points 33719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 17877 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) : 0.6402763 object centre at (A) : -0.1559992 29.67300 15.69050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0827939E-02 3.0616522E-02 midg,1,midg; midg,igrid,midg -1.2003348E-03 2.2451995E-02 1,midg,midg; igrid,midg,midg 4.8284091E-02 4.5144949E-02 gauss-seidel spectral radius is 0.9986534 estimated iterations to convergence 216 setup time was (sec) 0.6000000 now iterating at: 00:06:08 rms-change max change #iterations 4.020632 166.5614 at 10iterations 1.884528 89.47997 at 20iterations 0.8858562 31.51628 at 30iterations 0.4146240 12.94808 at 40iterations 0.1951623 6.039293 at 50iterations 9.1534264E-02 2.866152 at 60iterations 4.3127757E-02 1.443108 at 70iterations 2.0206699E-02 0.6441956 at 80iterations 9.5179873E-03 0.3086958 at 90iterations 4.4717770E-03 0.1451294 at 100iterations 2.1034856E-03 6.7428589E-02 at 110iterations 9.8681985E-04 3.3763885E-02 at 120iterations finished qdiffx linear iterations at : 00:06:16 total time elapsed so far: 8.140000 # loops : 120 mean,max change (kT/e) : 9.8681985E-04 3.3763885E-02 energy calculations done at 8.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.270000 DelPhi exited at 00:06:16 8.276u 0.229s 0:08.85 95.9% 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 Sun Oct 9 2011 at 00:06:16 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 = 2407 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: 2.881243 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): -26.98100 26.66900 ymin,ymax (A): 8.019000 51.32700 zmin,zma (A): -12.11000 43.49100 x,y,z range (A): 53.65000 43.30800 55.60100 scale (grids/A): 2.881243 object centre (A): -0.1559992 29.67300 15.69050 number of atom coordinates read : 2407 total number of charged atoms : 2272 net assigned charge : 10.50003 assigned positive charge : 350.1793 centred at (gu) : 92.71145 91.83738 93.41802 assigned negative charge : -339.6801 centred at (gu) : 92.86933 91.54117 93.66433 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 168804 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23171 grid for indexing accessible points = 1.400000 m= 82702 mr = 118659 m= 29910 mr = 65759 m= 7357 mr = 23373 m= 1229 mr = 5353 m= 78 mr = 850 m= 0 mr = 21 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 7138 time to turn everything in is 0.9400000 number of dielectric boundary points 76065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 18170 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) : 1.920829 object centre at (A) : -0.1559992 29.67300 15.69050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9646662 0.3701155 midg,1,midg; midg,igrid,midg -3.6895864E-02 0.2201533 1,midg,midg; igrid,midg,midg 0.4911754 0.4329398 gauss-seidel spectral radius is 0.9992726 estimated iterations to convergence 293 setup time was (sec) 1.200000 now iterating at: 00:06:18 rms-change max change #iterations 9.546453 381.5290 at 10iterations 5.636919 140.0455 at 20iterations 3.306329 81.99538 at 30iterations 1.929846 41.11847 at 40iterations 1.124987 22.33575 at 50iterations 0.6523820 15.08226 at 60iterations 0.3801763 8.495222 at 70iterations 0.2196964 4.655037 at 80iterations 0.1273935 2.411396 at 90iterations 7.3757514E-02 1.469766 at 100iterations 4.2702291E-02 0.7824898 at 110iterations 2.4617471E-02 0.4786439 at 120iterations 1.4237101E-02 0.2912521 at 130iterations 8.2273688E-03 0.1518848 at 140iterations 4.7543272E-03 9.1010571E-02 at 150iterations 2.7394127E-03 5.6427002E-02 at 160iterations 1.5840245E-03 2.8002739E-02 at 170iterations 9.1408292E-04 1.7349243E-02 at 180iterations finished qdiffx linear iterations at : 00:06:30 total time elapsed so far: 13.35000 # loops : 180 mean,max change (kT/e) : 9.1408292E-04 1.7349243E-02 energy calculations done at 13.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 00:06:30 13.481u 0.256s 0:14.07 97.5% 0+0k 0+0io 0pf+0w