Wed Nov 16 12:04:34 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 Nov 16 2011 at 12:04:34 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 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: 0.7501528 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): -21.00800 24.26100 ymin,ymax (A): -8.010000 36.26100 zmin,zma (A): -3.377000 44.08000 x,y,z range (A): 45.26900 44.27100 47.45700 scale (grids/A): 0.7501528 object centre (A): 1.626500 14.12550 20.35150 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -7.999989 assigned positive charge : 316.8519 centred at (gu) : 89.09353 90.41959 90.22121 assigned negative charge : -324.8520 centred at (gu) : 89.10335 90.50439 90.40393 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8283 nv = 96 ne = 84 npr = 43758 no. pairs analyzed = 43758 no. exposed pairs = 2735 no. arc points = 19239 no. surface atoms = 923 nbur = 1192 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 596 mr = 4621 m= 7 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.2200000 number of dielectric boundary points 4153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1515 ## 129 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8599 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0542116E-08 -4.2591770E-07 midg,1,midg; midg,igrid,midg -6.3163064E-08 -3.0436289E-07 1,midg,midg; igrid,midg,midg -1.8966509E-07 -1.5856547E-07 gauss-seidel spectral radius is 0.9907405 estimated iterations to convergence 84 setup time was (sec) 0.4200000 now iterating at: 12:04:35 rms-change max change #iterations 0.2605858 37.53904 at 10iterations 3.6460090E-02 4.804865 at 20iterations 4.9468717E-03 0.7044375 at 30iterations 6.9153798E-04 7.9064846E-02 at 40iterations 9.6065087E-05 1.1367798E-02 at 50iterations finished qdiffx linear iterations at : 12:04:38 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 9.6065087E-05 1.1367798E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 12:04:38 3.503u 0.183s 0:04.08 90.1% 0+0k 0+45632io 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 Nov 16 2011 at 12:04:38 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 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: 2.250458 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): -21.00800 24.26100 ymin,ymax (A): -8.010000 36.26100 zmin,zma (A): -3.377000 44.08000 x,y,z range (A): 45.26900 44.27100 47.45700 scale (grids/A): 2.250458 object centre (A): 1.626500 14.12550 20.35150 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -7.999989 assigned positive charge : 316.8519 centred at (gu) : 87.28049 91.25874 90.66389 assigned negative charge : -324.8520 centred at (gu) : 87.31013 91.51308 91.21186 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 86791 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19239 grid for indexing accessible points = 1.400000 m= 35134 mr = 60094 m= 7647 mr = 26483 m= 879 mr = 5326 m= 26 mr = 474 m= 0 mr = 2 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1546 time to turn everything in is 0.5500000 number of dielectric boundary points 38098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 15759 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) : 0.7501528 object centre at (A) : 1.626500 14.12550 20.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6600816E-02 -0.1708460 midg,1,midg; midg,igrid,midg -2.9173050E-02 -4.8988301E-02 1,midg,midg; igrid,midg,midg -4.4308338E-02 -9.2472034E-03 gauss-seidel spectral radius is 0.9989516 estimated iterations to convergence 244 setup time was (sec) 0.7600000 now iterating at: 12:04:39 rms-change max change #iterations 5.273574 213.9183 at 10iterations 2.697331 89.42847 at 20iterations 1.386287 46.42365 at 30iterations 0.7106256 20.76975 at 40iterations 0.3652594 11.30871 at 50iterations 0.1880817 5.603343 at 60iterations 9.6601591E-02 3.068828 at 70iterations 4.9469616E-02 1.401636 at 80iterations 2.5420344E-02 0.6831875 at 90iterations 1.3127862E-02 0.3546357 at 100iterations 6.7173908E-03 0.1930377 at 110iterations 3.4570796E-03 0.1022091 at 120iterations finished qdiffx linear iterations at : 12:04:46 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 3.4570796E-03 0.1022091 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 12:04:47 8.181u 0.212s 0:08.69 96.5% 0+0k 0+45168io 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 Nov 16 2011 at 12:04:47 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 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: 3.375687 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): -21.00800 24.26100 ymin,ymax (A): -8.010000 36.26100 zmin,zma (A): -3.377000 44.08000 x,y,z range (A): 45.26900 44.27100 47.45700 scale (grids/A): 3.375687 object centre (A): 1.626500 14.12550 20.35150 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -7.999989 assigned positive charge : 316.8519 centred at (gu) : 85.92102 91.88809 90.99564 assigned negative charge : -324.8520 centred at (gu) : 85.96518 92.26952 91.81781 start vw surface at 0.1000000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 199867 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19239 grid for indexing accessible points = 1.400000 m= 107420 mr = 144563 m= 46233 mr = 88987 m= 14699 mr = 38085 m= 3442 mr = 11598 m= 454 mr = 2549 m= 26 mr = 273 m= 0 mr = 3 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 5012 time to turn everything in is 1.730000 number of dielectric boundary points 86083 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 15808 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) : 2.250458 object centre at (A) : 1.626500 14.12550 20.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6756952E-03 -1.470094 midg,1,midg; midg,igrid,midg -0.2510912 -0.3481002 1,midg,midg; igrid,midg,midg -0.5289511 -7.6087520E-02 gauss-seidel spectral radius is 0.9993269 estimated iterations to convergence 304 setup time was (sec) 1.970000 now iterating at: 12:04:49 rms-change max change #iterations 11.27457 284.4978 at 10iterations 6.677664 128.5495 at 20iterations 3.962627 70.07115 at 30iterations 2.342640 38.06544 at 40iterations 1.384090 23.74523 at 50iterations 0.8161510 13.63447 at 60iterations 0.4822357 8.067801 at 70iterations 0.2845360 4.723125 at 80iterations 0.1675558 2.575120 at 90iterations 9.8786317E-02 1.620047 at 100iterations 5.8164187E-02 0.9047432 at 110iterations 3.4330685E-02 0.5195808 at 120iterations 2.0206446E-02 0.3122654 at 130iterations 1.1923545E-02 0.1843014 at 140iterations 7.0277392E-03 0.1069922 at 150iterations 4.1364753E-03 6.6896439E-02 at 160iterations 2.4401685E-03 3.7980318E-02 at 170iterations 1.4333021E-03 2.3061275E-02 at 180iterations finished qdiffx linear iterations at : 12:05:01 total time elapsed so far: 13.54000 # loops : 180 mean,max change (kT/e) : 1.4333021E-03 2.3061275E-02 energy calculations done at 13.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.68000 DelPhi exited at 12:05:01 13.686u 0.232s 0:14.20 97.9% 0+0k 0+45160io 0pf+0w