Sat Oct 8 21:20:34 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 Sat Oct 8 2011 at 21:20:34 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! 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: ZN5 556 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6150337 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): -31.41900 17.41700 ymin,ymax (A): -23.66900 22.51300 zmin,zma (A): -12.50300 45.38000 x,y,z range (A): 48.83600 46.18200 57.88300 scale (grids/A): 0.6150337 object centre (A): -7.001000 -0.5779991 16.43850 number of atom coordinates read : 2573 total number of charged atoms : 2454 net assigned charge : 4.000010 assigned positive charge : 393.0041 centred at (gu) : 88.50883 89.28640 89.55357 assigned negative charge : -389.0045 centred at (gu) : 88.40863 89.33998 89.45285 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6299 nv = 96 ne = 84 npr = 53521 no. pairs analyzed = 53521 no. exposed pairs = 3010 no. arc points = 21952 no. surface atoms = 996 nbur = 1577 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 291 mr = 3474 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 126 time to turn everything in is 0.2100000 number of dielectric boundary points 3091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2206 ## 239 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7924 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3215710E-09 7.7730027E-09 midg,1,midg; midg,igrid,midg 6.9365433E-09 -1.7807829E-10 1,midg,midg; igrid,midg,midg -4.2261470E-09 6.1579399E-09 gauss-seidel spectral radius is 0.9863052 estimated iterations to convergence 70 setup time was (sec) 0.4200000 now iterating at: 21:20:34 rms-change max change #iterations 0.1232852 21.78313 at 10iterations 1.1123551E-02 1.711870 at 20iterations 9.9111570E-04 0.1349897 at 30iterations 8.8501663E-05 1.3267517E-02 at 40iterations 8.1221569E-06 1.2702942E-03 at 50iterations finished qdiffx linear iterations at : 21:20:37 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 8.1221569E-06 1.2702942E-03 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.720000 DelPhi exited at 21:20:38 3.722u 0.198s 0:04.27 91.5% 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 Sat Oct 8 2011 at 21:20:38 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! 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: ZN5 556 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.845101 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): -31.41900 17.41700 ymin,ymax (A): -23.66900 22.51300 zmin,zma (A): -12.50300 45.38000 x,y,z range (A): 48.83600 46.18200 57.88300 scale (grids/A): 1.845101 object centre (A): -7.001000 -0.5779991 16.43850 number of atom coordinates read : 2573 total number of charged atoms : 2454 net assigned charge : 4.000010 assigned positive charge : 393.0041 centred at (gu) : 85.52605 87.85883 88.66022 assigned negative charge : -389.0045 centred at (gu) : 85.22569 88.01967 88.35806 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21952 grid for indexing accessible points = 1.400000 m= 22617 mr = 48059 m= 2901 mr = 16444 m= 138 mr = 1735 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 4049 time to turn everything in is 0.3300000 number of dielectric boundary points 28465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 19221 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) : 0.6150337 object centre at (A) : -7.001000 -0.5779991 16.43850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4299859E-02 1.9419480E-02 midg,1,midg; midg,igrid,midg 1.2953805E-02 1.1938752E-03 1,midg,midg; igrid,midg,midg -7.1405298E-03 3.0649090E-02 gauss-seidel spectral radius is 0.9985427 estimated iterations to convergence 208 setup time was (sec) 0.5300000 now iterating at: 21:20:39 rms-change max change #iterations 4.003852 174.1023 at 10iterations 1.825400 62.93090 at 20iterations 0.8356137 32.25337 at 30iterations 0.3806513 13.95162 at 40iterations 0.1737430 6.054646 at 50iterations 7.9583399E-02 2.826645 at 60iterations 3.6220346E-02 1.198377 at 70iterations 1.6604688E-02 0.5234604 at 80iterations 7.5498680E-03 0.2967606 at 90iterations 3.4663940E-03 0.1120522 at 100iterations 1.5843618E-03 6.1375618E-02 at 110iterations 7.2497042E-04 2.9941559E-02 at 120iterations finished qdiffx linear iterations at : 21:20:46 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 7.2497042E-04 2.9941559E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 21:20:46 7.974u 0.231s 0:08.52 96.2% 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 Sat Oct 8 2011 at 21:20:46 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! 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: ZN5 556 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.767652 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): -31.41900 17.41700 ymin,ymax (A): -23.66900 22.51300 zmin,zma (A): -12.50300 45.38000 x,y,z range (A): 48.83600 46.18200 57.88300 scale (grids/A): 2.767652 object centre (A): -7.001000 -0.5779991 16.43850 number of atom coordinates read : 2573 total number of charged atoms : 2454 net assigned charge : 4.000010 assigned positive charge : 393.0041 centred at (gu) : 83.28894 86.78812 87.99021 assigned negative charge : -389.0045 centred at (gu) : 82.83852 87.02943 87.53705 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 160144 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21952 grid for indexing accessible points = 1.400000 m= 76697 mr = 116474 m= 24283 mr = 62795 m= 4990 mr = 19172 m= 537 mr = 3601 m= 28 mr = 329 m= 0 mr = 7 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 13440 time to turn everything in is 0.8500000 number of dielectric boundary points 64301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 19628 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) : 1.845101 object centre at (A) : -7.001000 -0.5779991 16.43850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0054941E-02 0.2232587 midg,1,midg; midg,igrid,midg 0.1683418 -1.2677752E-02 1,midg,midg; igrid,midg,midg -6.9952101E-02 0.4041496 gauss-seidel spectral radius is 0.9992272 estimated iterations to convergence 284 setup time was (sec) 1.080000 now iterating at: 21:20:48 rms-change max change #iterations 9.380807 341.4195 at 10iterations 5.368150 121.2861 at 20iterations 3.057022 78.49518 at 30iterations 1.740397 36.15142 at 40iterations 0.9879069 22.45002 at 50iterations 0.5616524 11.31293 at 60iterations 0.3183362 6.104009 at 70iterations 0.1802910 3.624664 at 80iterations 0.1025567 1.996298 at 90iterations 5.8057658E-02 1.169235 at 100iterations 3.2990087E-02 0.6282234 at 110iterations 1.8698020E-02 0.3541479 at 120iterations 1.0601251E-02 0.1912374 at 130iterations 6.0110861E-03 0.1270409 at 140iterations 3.4115575E-03 5.8623314E-02 at 150iterations 1.9396406E-03 3.7468433E-02 at 160iterations 1.0975342E-03 2.1400452E-02 at 170iterations 6.2320830E-04 1.1875153E-02 at 180iterations finished qdiffx linear iterations at : 21:20:59 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 6.2320830E-04 1.1875153E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 21:21:00 12.772u 0.315s 0:13.39 97.6% 0+0k 0+0io 0pf+0w