Mon Oct 10 22:03:28 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 Mon Oct 10 2011 at 22:03:28 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 = 2826 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: 0.5630684 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): -23.79200 32.72700 ymin,ymax (A): -33.14900 23.72800 zmin,zma (A): -6.407000 56.81800 x,y,z range (A): 56.51900 56.87700 63.22500 scale (grids/A): 0.5630684 object centre (A): 4.467501 -4.710502 25.20550 number of atom coordinates read : 2826 total number of charged atoms : 2746 net assigned charge : 2.500006 assigned positive charge : 418.9402 centred at (gu) : 89.28329 89.06467 90.75289 assigned negative charge : -416.4415 centred at (gu) : 89.11669 89.13505 90.68315 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6119 nv = 96 ne = 84 npr = 54740 no. pairs analyzed = 54740 no. exposed pairs = 3888 no. arc points = 27710 no. surface atoms = 1307 nbur = 1519 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 243 mr = 3012 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2806 ## 330 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7819 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2438850E-10 1.3187346E-09 midg,1,midg; midg,igrid,midg 1.3878858E-09 -4.1143119E-10 1,midg,midg; igrid,midg,midg -1.9884974E-09 1.8372394E-09 gauss-seidel spectral radius is 0.9837305 estimated iterations to convergence 64 setup time was (sec) 0.6200000 now iterating at: 22:03:29 rms-change max change #iterations 8.0081820E-02 18.07526 at 10iterations 5.8496338E-03 0.9662476 at 20iterations 5.3896749E-04 8.9973450E-02 at 30iterations 7.9815043E-05 1.1420250E-02 at 40iterations 1.6310349E-05 2.3298264E-03 at 50iterations finished qdiffx linear iterations at : 22:03:33 total time elapsed so far: 4.910000 # loops : 50 mean,max change (kT/e) : 1.6310349E-05 2.3298264E-03 energy calculations done at 4.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.090000 DelPhi exited at 22:03:34 5.095u 0.446s 0:06.15 89.9% 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 Mon Oct 10 2011 at 22:03:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 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: 1.689205 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): -23.79200 32.72700 ymin,ymax (A): -33.14900 23.72800 zmin,zma (A): -6.407000 56.81800 x,y,z range (A): 56.51900 56.87700 63.22500 scale (grids/A): 1.689205 object centre (A): 4.467501 -4.710502 25.20550 number of atom coordinates read : 2826 total number of charged atoms : 2746 net assigned charge : 2.500006 assigned positive charge : 418.9402 centred at (gu) : 87.84906 87.19298 92.25755 assigned negative charge : -416.4415 centred at (gu) : 87.34995 87.40501 92.04916 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66883 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27710 grid for indexing accessible points = 1.400000 m= 20226 mr = 43739 m= 2392 mr = 13456 m= 82 mr = 1235 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 134 time to turn everything in is 0.5900000 number of dielectric boundary points 31147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 294 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 21192 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) : 0.5630684 object centre at (A) : 4.467501 -4.710502 25.20550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0322714E-04 1.2744868E-02 midg,1,midg; midg,igrid,midg 3.5115667E-03 -1.0192545E-02 1,midg,midg; igrid,midg,midg -1.3850830E-02 2.2756089E-02 gauss-seidel spectral radius is 0.9983103 estimated iterations to convergence 193 setup time was (sec) 0.9800000 now iterating at: 22:03:35 rms-change max change #iterations 3.454762 180.9173 at 10iterations 1.477047 86.45679 at 20iterations 0.6347769 28.07476 at 30iterations 0.2718359 9.790207 at 40iterations 0.1175326 4.231308 at 50iterations 5.0291646E-02 1.996886 at 60iterations 2.1520417E-02 0.7758827 at 70iterations 9.2935786E-03 0.3083124 at 80iterations 3.9983885E-03 0.1397491 at 90iterations 1.7271552E-03 5.9285402E-02 at 100iterations 7.4641127E-04 2.5367737E-02 at 110iterations 3.2450928E-04 1.1102676E-02 at 120iterations finished qdiffx linear iterations at : 22:03:46 total time elapsed so far: 12.01000 # loops : 120 mean,max change (kT/e) : 3.2450928E-04 1.1102676E-02 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 22:03:47 12.183u 0.509s 0:12.99 97.6% 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 22:03:47 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 = 2826 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: 2.533808 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): -23.79200 32.72700 ymin,ymax (A): -33.14900 23.72800 zmin,zma (A): -6.407000 56.81800 x,y,z range (A): 56.51900 56.87700 63.22500 scale (grids/A): 2.533808 object centre (A): 4.467501 -4.710502 25.20550 number of atom coordinates read : 2826 total number of charged atoms : 2746 net assigned charge : 2.500006 assigned positive charge : 418.9402 centred at (gu) : 86.77352 85.78933 93.38608 assigned negative charge : -416.4415 centred at (gu) : 86.02483 86.10740 93.07363 start vw surface at 0.1100000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 155391 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27710 grid for indexing accessible points = 1.400000 m= 69124 mr = 107660 m= 20747 mr = 53345 m= 3816 mr = 15459 m= 275 mr = 2511 m= 6 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 421 time to turn everything in is 1.390000 number of dielectric boundary points 70266 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 21953 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) : 1.689205 object centre at (A) : 4.467501 -4.710502 25.20550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1733459 0.2801161 midg,1,midg; midg,igrid,midg 5.8396228E-02 -0.1314252 1,midg,midg; igrid,midg,midg -0.3131019 0.3296306 gauss-seidel spectral radius is 0.9991852 estimated iterations to convergence 277 setup time was (sec) 1.760000 now iterating at: 22:03:49 rms-change max change #iterations 8.841854 328.4100 at 10iterations 5.066156 135.3819 at 20iterations 2.879728 71.83257 at 30iterations 1.635148 34.20589 at 40iterations 0.9236816 20.06319 at 50iterations 0.5202653 10.64063 at 60iterations 0.2920966 5.931881 at 70iterations 0.1642798 3.318836 at 80iterations 9.1856971E-02 1.841080 at 90iterations 5.1527925E-02 1.061701 at 100iterations 2.8824598E-02 0.5736790 at 110iterations 1.6128775E-02 0.3368912 at 120iterations 9.0297572E-03 0.1750097 at 130iterations 5.0502960E-03 0.1055775 at 140iterations 2.8239605E-03 6.5785885E-02 at 150iterations 1.5811775E-03 3.2943726E-02 at 160iterations 8.8400068E-04 1.8074036E-02 at 170iterations 4.9606315E-04 9.4108582E-03 at 180iterations finished qdiffx linear iterations at : 22:04:07 total time elapsed so far: 20.09000 # loops : 180 mean,max change (kT/e) : 4.9606315E-04 9.4108582E-03 energy calculations done at 20.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.26000 DelPhi exited at 22:04:08 20.261u 0.557s 0:21.08 98.7% 0+0k 0+0io 0pf+0w