Sat Oct 15 14:59:04 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 15 2011 at 14:59:04 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 = 2689 !!! WARNING: MET 254 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5929183 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): -26.02100 28.23700 ymin,ymax (A): -32.65400 25.19800 zmin,zma (A): -20.33900 39.70300 x,y,z range (A): 54.25800 57.85200 60.04200 scale (grids/A): 0.5929183 object centre (A): 1.108000 -3.728000 9.682002 number of atom coordinates read : 2689 total number of charged atoms : 2551 net assigned charge : 5.228011 assigned positive charge : 396.1616 centred at (gu) : 90.12646 90.78515 87.52800 assigned negative charge : -390.9348 centred at (gu) : 90.13316 90.77307 87.42234 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6121 nv = 96 ne = 84 npr = 54314 no. pairs analyzed = 54314 no. exposed pairs = 3609 no. arc points = 25179 no. surface atoms = 1206 nbur = 1483 mkacc time = 0.1300000 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 = 1.484000 m= 295 mr = 3025 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2593 ## 290 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7898 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3934783E-09 2.7971938E-09 midg,1,midg; midg,igrid,midg 1.2558666E-09 2.6212728E-09 1,midg,midg; igrid,midg,midg 1.9827873E-09 1.6954170E-09 gauss-seidel spectral radius is 0.9852920 estimated iterations to convergence 68 setup time was (sec) 0.5600000 now iterating at: 14:59:04 rms-change max change #iterations 0.1031596 17.89901 at 10iterations 8.5467044E-03 1.513033 at 20iterations 7.0861832E-04 0.1041679 at 30iterations 6.0497270E-05 9.0980530E-03 at 40iterations 5.8133937E-06 8.6784363E-04 at 50iterations finished qdiffx linear iterations at : 14:59:07 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 5.8133937E-06 8.6784363E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 14:59:08 3.432u 0.159s 0:04.09 87.5% 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 Sat Oct 15 2011 at 14:59:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2689 !!! WARNING: MET 254 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.778755 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): -26.02100 28.23700 ymin,ymax (A): -32.65400 25.19800 zmin,zma (A): -20.33900 39.70300 x,y,z range (A): 54.25800 57.85200 60.04200 scale (grids/A): 1.778755 object centre (A): 1.108000 -3.728000 9.682002 number of atom coordinates read : 2689 total number of charged atoms : 2551 net assigned charge : 5.228011 assigned positive charge : 396.1616 centred at (gu) : 90.37877 92.35471 82.58348 assigned negative charge : -390.9348 centred at (gu) : 90.39948 92.31915 82.26698 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 66346 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25179 grid for indexing accessible points = 1.400000 m= 21248 mr = 43546 m= 2925 mr = 14393 m= 140 mr = 1559 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 131 time to turn everything in is 0.5200000 number of dielectric boundary points 31121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19917 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) : 0.5929183 object centre at (A) : 1.108000 -3.728000 9.682002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7746406E-02 3.0935349E-02 midg,1,midg; midg,igrid,midg 3.1969699E-03 -8.8439789E-03 1,midg,midg; igrid,midg,midg 2.8952312E-02 1.7833628E-02 gauss-seidel spectral radius is 0.9984511 estimated iterations to convergence 202 setup time was (sec) 0.8100000 now iterating at: 14:59:09 rms-change max change #iterations 3.741520 161.4135 at 10iterations 1.663538 66.74575 at 20iterations 0.7421656 27.12192 at 30iterations 0.3317257 12.22783 at 40iterations 0.1479756 5.446643 at 50iterations 6.5561876E-02 2.372445 at 60iterations 2.9384758E-02 1.027232 at 70iterations 1.3085147E-02 0.4656544 at 80iterations 5.8148867E-03 0.2005692 at 90iterations 2.6001956E-03 9.8518372E-02 at 100iterations 1.1566689E-03 3.7333488E-02 at 110iterations 5.1778340E-04 1.6777992E-02 at 120iterations finished qdiffx linear iterations at : 14:59:15 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 5.1778340E-04 1.6777992E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 14:59:16 7.557u 0.193s 0:08.02 96.5% 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 15 2011 at 14:59:16 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 = 2689 !!! WARNING: MET 254 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.668132 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): -26.02100 28.23700 ymin,ymax (A): -32.65400 25.19800 zmin,zma (A): -20.33900 39.70300 x,y,z range (A): 54.25800 57.85200 60.04200 scale (grids/A): 2.668132 object centre (A): 1.108000 -3.728000 9.682002 number of atom coordinates read : 2689 total number of charged atoms : 2551 net assigned charge : 5.228011 assigned positive charge : 396.1616 centred at (gu) : 90.56802 93.53186 78.87495 assigned negative charge : -390.9348 centred at (gu) : 90.59904 93.47871 78.40059 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 153591 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25179 grid for indexing accessible points = 1.400000 m= 70406 mr = 106610 m= 23082 mr = 54664 m= 4815 mr = 17408 m= 558 mr = 3307 m= 28 mr = 313 m= 0 mr = 3 time to grow re-entrant surface = 0.6900000 no. cavity mid-points inaccessible to solvent = 474 time to turn everything in is 1.260000 number of dielectric boundary points 70175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 20402 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) : 1.778755 object centre at (A) : 1.108000 -3.728000 9.682002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6801484 0.6243904 midg,1,midg; midg,igrid,midg 1.9921038E-02 -8.9266405E-02 1,midg,midg; igrid,midg,midg 0.6161084 0.1610384 gauss-seidel spectral radius is 0.9992182 estimated iterations to convergence 282 setup time was (sec) 1.560000 now iterating at: 14:59:18 rms-change max change #iterations 9.177033 272.8027 at 10iterations 5.322423 144.9106 at 20iterations 3.052844 71.97833 at 30iterations 1.746528 42.45209 at 40iterations 0.9976089 23.42672 at 50iterations 0.5656029 11.51645 at 60iterations 0.3210873 6.733519 at 70iterations 0.1820101 3.872185 at 80iterations 0.1031318 2.434484 at 90iterations 5.8286600E-02 1.165422 at 100iterations 3.2958567E-02 0.6475334 at 110iterations 1.8658906E-02 0.3501663 at 120iterations 1.0530688E-02 0.2064552 at 130iterations 5.9598521E-03 0.1161032 at 140iterations 3.3690331E-03 6.7245483E-02 at 150iterations 1.9060730E-03 3.6598206E-02 at 160iterations 1.0766548E-03 1.9723892E-02 at 170iterations 6.0819933E-04 1.2022972E-02 at 180iterations finished qdiffx linear iterations at : 14:59:28 total time elapsed so far: 11.95000 # loops : 180 mean,max change (kT/e) : 6.0819933E-04 1.2022972E-02 energy calculations done at 11.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.15000 DelPhi exited at 14:59:29 12.148u 0.173s 0:12.68 97.0% 0+0k 0+0io 0pf+0w