Tue Oct 11 06:16:41 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 Tue Oct 11 2011 at 06:16:42 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 = 1988 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: 0.7252873 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): -19.97600 24.58500 ymin,ymax (A): -10.60800 27.56100 zmin,zma (A): -3.083000 46.00100 x,y,z range (A): 44.56100 38.16900 49.08400 scale (grids/A): 0.7252873 object centre (A): 2.304501 8.476501 21.45900 number of atom coordinates read : 1988 total number of charged atoms : 1874 net assigned charge : 5.500006 assigned positive charge : 301.4581 centred at (gu) : 89.63551 89.05656 91.12241 assigned negative charge : -295.9583 centred at (gu) : 89.46604 89.13015 91.16055 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7271 nv = 96 ne = 84 npr = 39340 no. pairs analyzed = 39340 no. exposed pairs = 2501 no. arc points = 17120 no. surface atoms = 854 nbur = 1134 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 529 mr = 4169 m= 6 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3517 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1538 ## 134 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7780 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8397214E-08 5.3568840E-08 midg,1,midg; midg,igrid,midg 1.4440687E-07 1.6598634E-08 1,midg,midg; igrid,midg,midg -5.2552547E-08 1.7295046E-07 gauss-seidel spectral radius is 0.9900801 estimated iterations to convergence 82 setup time was (sec) 0.5500000 now iterating at: 06:16:43 rms-change max change #iterations 0.2159406 30.64618 at 10iterations 2.7978482E-02 4.004662 at 20iterations 3.8220710E-03 0.4594340 at 30iterations 6.1065005E-04 9.0097427E-02 at 40iterations 1.3986143E-04 1.8503189E-02 at 50iterations finished qdiffx linear iterations at : 06:16:47 total time elapsed so far: 4.790000 # loops : 50 mean,max change (kT/e) : 1.3986143E-04 1.8503189E-02 energy calculations done at 4.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.960000 DelPhi exited at 06:16:47 4.966u 0.464s 0:05.77 93.9% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 06:16:47 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 = 1988 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: 2.175862 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): -19.97600 24.58500 ymin,ymax (A): -10.60800 27.56100 zmin,zma (A): -3.083000 46.00100 x,y,z range (A): 44.56100 38.16900 49.08400 scale (grids/A): 2.175862 object centre (A): 2.304501 8.476501 21.45900 number of atom coordinates read : 1988 total number of charged atoms : 1874 net assigned charge : 5.500006 assigned positive charge : 301.4581 centred at (gu) : 88.90667 87.16964 93.36721 assigned negative charge : -295.9583 centred at (gu) : 88.39805 87.39069 93.48171 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 76270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17120 grid for indexing accessible points = 1.400000 m= 33049 mr = 54136 m= 7423 mr = 25526 m= 801 mr = 5201 m= 32 mr = 471 m= 0 mr = 8 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 32233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 14915 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) : 0.7252873 object centre at (A) : 2.304501 8.476501 21.45900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8733609E-02 1.0090065E-02 midg,1,midg; midg,igrid,midg 4.3443885E-02 1.1135486E-03 1,midg,midg; igrid,midg,midg 2.5793614E-02 4.5365185E-02 gauss-seidel spectral radius is 0.9988748 estimated iterations to convergence 236 setup time was (sec) 0.9800000 now iterating at: 06:16:49 rms-change max change #iterations 4.658292 187.8359 at 10iterations 2.340381 72.63255 at 20iterations 1.179476 44.26849 at 30iterations 0.5943441 18.09041 at 40iterations 0.2995382 8.815895 at 50iterations 0.1512669 4.452628 at 60iterations 7.5934455E-02 2.396325 at 70iterations 3.8533553E-02 1.248038 at 80iterations 1.9467589E-02 0.5733757 at 90iterations 9.8838760E-03 0.3289032 at 100iterations 5.0121145E-03 0.1522732 at 110iterations 2.5942023E-03 8.4793091E-02 at 120iterations finished qdiffx linear iterations at : 06:17:00 total time elapsed so far: 11.86000 # loops : 120 mean,max change (kT/e) : 2.5942023E-03 8.4793091E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 06:17:00 12.033u 0.528s 0:13.06 96.0% 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 Tue Oct 11 2011 at 06:17:00 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 = 1988 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: 3.263793 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): -19.97600 24.58500 ymin,ymax (A): -10.60800 27.56100 zmin,zma (A): -3.083000 46.00100 x,y,z range (A): 44.56100 38.16900 49.08400 scale (grids/A): 3.263793 object centre (A): 2.304501 8.476501 21.45900 number of atom coordinates read : 1988 total number of charged atoms : 1874 net assigned charge : 5.500006 assigned positive charge : 301.4581 centred at (gu) : 88.35999 85.75457 95.05093 assigned negative charge : -295.9583 centred at (gu) : 87.59717 86.08611 95.22259 start vw surface at 0.1000000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 175358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17120 grid for indexing accessible points = 1.400000 m= 99459 mr = 129772 m= 44460 mr = 83549 m= 14561 mr = 37277 m= 3196 mr = 11553 m= 425 mr = 2418 m= 19 mr = 307 m= 0 mr = 12 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.070000 number of dielectric boundary points 72590 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.240000 number of grid points assigned charge 14984 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) : 2.175862 object centre at (A) : 2.304501 8.476501 21.45900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1587121 5.8849189E-02 midg,1,midg; midg,igrid,midg 0.3318091 -2.0201521E-03 1,midg,midg; igrid,midg,midg 0.4908950 0.3637427 gauss-seidel spectral radius is 0.9993061 estimated iterations to convergence 299 setup time was (sec) 2.460000 now iterating at: 06:17:03 rms-change max change #iterations 10.29474 334.8869 at 10iterations 6.118511 134.0192 at 20iterations 3.631769 80.50298 at 30iterations 2.152442 42.95761 at 40iterations 1.276582 23.98778 at 50iterations 0.7534222 17.17725 at 60iterations 0.4437775 8.727536 at 70iterations 0.2613569 4.860895 at 80iterations 0.1538538 3.101921 at 90iterations 9.0836704E-02 1.621891 at 100iterations 5.3486526E-02 0.9301331 at 110iterations 3.1602561E-02 0.5999451 at 120iterations 1.8789219E-02 0.3313293 at 130iterations 1.1280074E-02 0.1932769 at 140iterations 6.9154468E-03 0.1247253 at 150iterations 4.3881708E-03 8.3614349E-02 at 160iterations 2.9308675E-03 5.2577972E-02 at 170iterations 2.0858070E-03 3.7977219E-02 at 180iterations finished qdiffx linear iterations at : 06:17:22 total time elapsed so far: 20.68000 # loops : 180 mean,max change (kT/e) : 2.0858070E-03 3.7977219E-02 energy calculations done at 20.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.84000 DelPhi exited at 06:17:22 20.846u 0.539s 0:21.82 97.9% 0+0k 0+0io 0pf+0w