Sat Oct 8 20:36:08 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 8 2011 at 20:36:08 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN2 264 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6241124 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): -32.32000 17.45500 ymin,ymax (A): -24.34200 22.68300 zmin,zma (A): -12.37200 44.66900 x,y,z range (A): 49.77500 47.02500 57.04100 scale (grids/A): 0.6241124 object centre (A): -7.432500 -0.8294992 16.14850 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.67073 89.24097 89.77693 assigned negative charge : -387.4045 centred at (gu) : 88.56752 89.28149 89.65793 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6628 nv = 96 ne = 84 npr = 54338 no. pairs analyzed = 54338 no. exposed pairs = 2990 no. arc points = 21297 no. surface atoms = 1005 nbur = 1589 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 359 mr = 3769 m= 0 mr = 54 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 201 time to turn everything in is 0.3600000 number of dielectric boundary points 3164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2133 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8144 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5019860E-09 1.1915333E-08 midg,1,midg; midg,igrid,midg 7.9844060E-09 6.4395489E-10 1,midg,midg; igrid,midg,midg -5.4996177E-09 8.5102627E-09 gauss-seidel spectral radius is 0.9866992 estimated iterations to convergence 71 setup time was (sec) 0.6300000 now iterating at: 20:36:09 rms-change max change #iterations 0.1304858 18.90777 at 10iterations 1.2215807E-02 1.915076 at 20iterations 1.1551934E-03 0.2023888 at 30iterations 1.0756228E-04 1.4976501E-02 at 40iterations 1.0093728E-05 1.4038086E-03 at 50iterations finished qdiffx linear iterations at : 20:36:12 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 1.0093728E-05 1.4038086E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 20:36:13 4.083u 0.249s 0:04.64 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 8 2011 at 20:36:13 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN2 264 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.872337 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): -32.32000 17.45500 ymin,ymax (A): -24.34200 22.68300 zmin,zma (A): -12.37200 44.66900 x,y,z range (A): 49.77500 47.02500 57.04100 scale (grids/A): 1.872337 object centre (A): -7.432500 -0.8294992 16.14850 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 86.01178 87.72240 89.33037 assigned negative charge : -387.4045 centred at (gu) : 85.70212 87.84431 88.97378 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72203 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21297 grid for indexing accessible points = 1.400000 m= 26257 mr = 50995 m= 3883 mr = 19786 m= 183 mr = 2449 m= 2 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 7900 time to turn everything in is 0.6500000 number of dielectric boundary points 29238 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 19262 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) : 0.6241124 object centre at (A) : -7.432500 -0.8294992 16.14850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7128538E-02 2.2144455E-02 midg,1,midg; midg,igrid,midg 1.0275811E-02 4.1177371E-03 1,midg,midg; igrid,midg,midg -6.0623875E-03 3.7079420E-02 gauss-seidel spectral radius is 0.9985850 estimated iterations to convergence 211 setup time was (sec) 0.9600000 now iterating at: 20:36:14 rms-change max change #iterations 4.086619 166.6107 at 10iterations 1.887053 71.83931 at 20iterations 0.8737621 27.39813 at 30iterations 0.4003023 13.72065 at 40iterations 0.1866428 6.428997 at 50iterations 8.6098686E-02 2.481210 at 60iterations 3.9814930E-02 1.346962 at 70iterations 1.8414754E-02 0.5843410 at 80iterations 8.5113002E-03 0.2921513 at 90iterations 3.9346055E-03 0.1294937 at 100iterations 1.8140996E-03 6.1061859E-02 at 110iterations 8.3986175E-04 2.7704239E-02 at 120iterations finished qdiffx linear iterations at : 20:36:22 total time elapsed so far: 9.220000 # loops : 120 mean,max change (kT/e) : 8.3986175E-04 2.7704239E-02 energy calculations done at 9.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.390000 DelPhi exited at 20:36:23 9.392u 0.272s 0:09.98 96.7% 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 8 2011 at 20:36:23 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN2 264 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.808506 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): -32.32000 17.45500 ymin,ymax (A): -24.34200 22.68300 zmin,zma (A): -12.37200 44.66900 x,y,z range (A): 49.77500 47.02500 57.04100 scale (grids/A): 2.808506 object centre (A): -7.432500 -0.8294992 16.14850 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 84.01749 86.58363 88.99543 assigned negative charge : -387.4045 centred at (gu) : 83.55315 86.76637 88.46046 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 166897 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21297 grid for indexing accessible points = 1.400000 m= 85740 mr = 122804 m= 30138 mr = 71307 m= 7062 mr = 24587 m= 881 mr = 5432 m= 41 mr = 579 m= 0 mr = 8 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 26453 time to turn everything in is 1.630000 number of dielectric boundary points 66042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 19631 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) : 1.872337 object centre at (A) : -7.432500 -0.8294992 16.14850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1530643 0.2593633 midg,1,midg; midg,igrid,midg 0.1317896 4.0819515E-02 1,midg,midg; igrid,midg,midg -4.6167314E-02 0.4440270 gauss-seidel spectral radius is 0.9992374 estimated iterations to convergence 286 setup time was (sec) 1.940000 now iterating at: 20:36:25 rms-change max change #iterations 9.527469 280.4079 at 10iterations 5.480327 138.6367 at 20iterations 3.139996 69.81221 at 30iterations 1.794550 38.65880 at 40iterations 1.026556 21.61764 at 50iterations 0.5842835 11.58637 at 60iterations 0.3334972 6.556757 at 70iterations 0.1904981 3.400640 at 80iterations 0.1087302 2.072022 at 90iterations 6.1844196E-02 1.221247 at 100iterations 3.5286382E-02 0.7791538 at 110iterations 2.0094870E-02 0.3462477 at 120iterations 1.1433729E-02 0.2057343 at 130iterations 6.5239482E-03 0.1325684 at 140iterations 3.7233983E-03 9.0429306E-02 at 150iterations 2.1219603E-03 4.4404984E-02 at 160iterations 1.2070957E-03 2.2071838E-02 at 170iterations 6.8989903E-04 1.2752533E-02 at 180iterations finished qdiffx linear iterations at : 20:36:39 total time elapsed so far: 15.44000 # loops : 180 mean,max change (kT/e) : 6.8989903E-04 1.2752533E-02 energy calculations done at 15.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.61000 DelPhi exited at 20:36:39 15.615u 0.318s 0:16.20 98.2% 0+0k 0+0io 0pf+0w