Wed Dec 21 14:20:58 PST 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 Wed Dec 21 2011 at 14:20:58 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5681636 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): -26.84300 35.81500 ymin,ymax (A): -18.95400 20.71900 zmin,zma (A): -3.147000 38.71200 x,y,z range (A): 62.65800 39.67300 41.85900 scale (grids/A): 0.5681636 object centre (A): 4.486001 0.8824997 17.78250 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 90.27850 90.18526 90.46159 assigned negative charge : -285.8263 centred at (gu) : 90.28793 90.28214 90.59982 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4204 nv = 96 ne = 84 npr = 40447 no. pairs analyzed = 40447 no. exposed pairs = 2418 no. arc points = 16969 no. surface atoms = 818 nbur = 1146 mkacc time = 6.0000002E-02 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= 142 mr = 2271 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2073 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1790 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 5297 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4207501E-09 -1.1610423E-09 midg,1,midg; midg,igrid,midg 1.1536124E-09 -6.6207356E-10 1,midg,midg; igrid,midg,midg 3.6263378E-10 2.2171880E-10 gauss-seidel spectral radius is 0.9839327 estimated iterations to convergence 65 setup time was (sec) 0.5300000 now iterating at: 14:20:59 rms-change max change #iterations 6.9485717E-02 11.50398 at 10iterations 5.2900272E-03 0.9647179 at 20iterations 3.8328682E-04 6.6135406E-02 at 30iterations 2.7714494E-05 5.8479309E-03 at 40iterations 2.1030382E-06 3.8909912E-04 at 50iterations finished qdiffx linear iterations at : 14:21:03 total time elapsed so far: 4.810000 # loops : 50 mean,max change (kT/e) : 2.1030382E-06 3.8909912E-04 energy calculations done at 4.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.940000 DelPhi exited at 14:21:04 4.949u 0.424s 0:06.42 83.4% 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 Wed Dec 21 2011 at 14:21:05 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.704491 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): -26.84300 35.81500 ymin,ymax (A): -18.95400 20.71900 zmin,zma (A): -3.147000 38.71200 x,y,z range (A): 62.65800 39.67300 41.85900 scale (grids/A): 1.704491 object centre (A): 4.486001 0.8824997 17.78250 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 90.83564 90.55554 91.38484 assigned negative charge : -285.8263 centred at (gu) : 90.86398 90.84663 91.79964 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 46402 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16969 grid for indexing accessible points = 1.400000 m= 15382 mr = 31712 m= 1563 mr = 11542 m= 33 mr = 851 m= 0 mr = 5 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 652 time to turn everything in is 0.2800000 number of dielectric boundary points 19270 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 211 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 14182 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) : 0.5681636 object centre at (A) : 4.486001 0.8824997 17.78250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1577319E-03 -7.4524232E-03 midg,1,midg; midg,igrid,midg 1.8970815E-03 -2.7334047E-03 1,midg,midg; igrid,midg,midg 2.6825245E-02 2.6988864E-02 gauss-seidel spectral radius is 0.9982151 estimated iterations to convergence 188 setup time was (sec) 0.7200000 now iterating at: 14:21:06 rms-change max change #iterations 2.813559 150.6604 at 10iterations 1.179366 62.12672 at 20iterations 0.4942655 21.76907 at 30iterations 0.2076822 9.206657 at 40iterations 8.7429151E-02 3.551159 at 50iterations 3.6635168E-02 1.612202 at 60iterations 1.5441000E-02 0.6641521 at 70iterations 6.4850408E-03 0.2573495 at 80iterations 2.7211837E-03 0.1096592 at 90iterations 1.1469994E-03 4.8755646E-02 at 100iterations 4.8113530E-04 2.0025253E-02 at 110iterations 2.0154814E-04 9.7465515E-03 at 120iterations finished qdiffx linear iterations at : 14:21:17 total time elapsed so far: 11.28000 # loops : 120 mean,max change (kT/e) : 2.0154814E-04 9.7465515E-03 energy calculations done at 11.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.41000 DelPhi exited at 14:21:21 11.417u 0.526s 0:16.43 72.6% 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 Wed Dec 21 2011 at 14:21:22 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.556736 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): -26.84300 35.81500 ymin,ymax (A): -18.95400 20.71900 zmin,zma (A): -3.147000 38.71200 x,y,z range (A): 62.65800 39.67300 41.85900 scale (grids/A): 2.556736 object centre (A): 4.486001 0.8824997 17.78250 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 91.25342 90.83345 92.07720 assigned negative charge : -285.8263 centred at (gu) : 91.29596 91.27007 92.69954 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 107420 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16969 grid for indexing accessible points = 1.400000 m= 52473 mr = 77090 m= 15971 mr = 43116 m= 2460 mr = 12900 m= 147 mr = 1725 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 2169 time to turn everything in is 0.6600000 number of dielectric boundary points 43579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 14650 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) : 1.704491 object centre at (A) : 4.486001 0.8824997 17.78250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6176789E-02 -8.5524440E-02 midg,1,midg; midg,igrid,midg 1.4286320E-02 -3.0852530E-02 1,midg,midg; igrid,midg,midg 0.3542215 0.3578930 gauss-seidel spectral radius is 0.9991133 estimated iterations to convergence 265 setup time was (sec) 1.040000 now iterating at: 14:21:25 rms-change max change #iterations 7.017487 264.1288 at 10iterations 3.849746 124.8926 at 20iterations 2.101199 60.14537 at 30iterations 1.146667 27.13110 at 40iterations 0.6242580 14.80148 at 50iterations 0.3389425 7.581284 at 60iterations 0.1843480 4.125486 at 70iterations 0.1001244 2.455429 at 80iterations 5.4495391E-02 1.256203 at 90iterations 2.9684233E-02 0.6779747 at 100iterations 1.6066032E-02 0.3871212 at 110iterations 8.7766051E-03 0.2053399 at 120iterations 4.7658663E-03 0.1125371 at 130iterations 2.5825573E-03 7.0268154E-02 at 140iterations 1.4043667E-03 3.1657219E-02 at 150iterations 7.6395925E-04 1.9034266E-02 at 160iterations 4.1608652E-04 9.3231201E-03 at 170iterations 2.2605377E-04 5.2833557E-03 at 180iterations finished qdiffx linear iterations at : 14:21:36 total time elapsed so far: 12.14000 # loops : 180 mean,max change (kT/e) : 2.2605377E-04 5.2833557E-03 energy calculations done at 12.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 14:21:43 12.272u 0.463s 0:20.75 61.3% 0+0k 0+0io 0pf+0w