Sat Oct 8 11:37:16 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 8 2011 at 11:37:16 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 = 4461 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5627658 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): -28.78800 34.47100 ymin,ymax (A): 34.51100 95.41400 zmin,zma (A): 31.42300 89.17000 x,y,z range (A): 63.25900 60.90300 57.74699 scale (grids/A): 0.5627658 object centre (A): 2.841500 64.96250 60.29650 number of atom coordinates read : 4461 total number of charged atoms : 4302 net assigned charge : -5.499955 assigned positive charge : 670.7770 centred at (gu) : 91.59528 89.61614 89.19310 assigned negative charge : -676.2803 centred at (gu) : 91.52868 89.72675 89.35893 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8881 nv = 96 ne = 84 npr = 94150 no. pairs analyzed = 94150 no. exposed pairs = 5068 no. arc points = 34346 no. surface atoms = 1717 nbur = 2744 mkacc time = 0.2500000 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 = 1.540000 m= 360 mr = 5098 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 118 time to turn everything in is 0.4700000 number of dielectric boundary points 4122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3569 ## 435 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 11856 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8268019E-09 -3.1567402E-09 midg,1,midg; midg,igrid,midg 1.4559798E-09 -2.5322830E-09 1,midg,midg; igrid,midg,midg -1.3288517E-09 7.9574602E-10 gauss-seidel spectral radius is 0.9838133 estimated iterations to convergence 65 setup time was (sec) 0.7300000 now iterating at: 11:37:17 rms-change max change #iterations 0.1063982 14.44528 at 10iterations 8.1256805E-03 1.226233 at 20iterations 7.9501473E-04 0.1022935 at 30iterations 1.6286901E-04 2.3259401E-02 at 40iterations 5.1967090E-05 8.0306530E-03 at 50iterations finished qdiffx linear iterations at : 11:37:21 total time elapsed so far: 4.420000 # loops : 50 mean,max change (kT/e) : 5.1967090E-05 8.0306530E-03 energy calculations done at 4.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.650000 DelPhi exited at 11:37:22 4.659u 0.426s 0:05.81 87.2% 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 8 2011 at 11:37:22 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 = 4461 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.688297 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): -28.78800 34.47100 ymin,ymax (A): 34.51100 95.41400 zmin,zma (A): 31.42300 89.17000 x,y,z range (A): 63.25900 60.90300 57.74699 scale (grids/A): 1.688297 object centre (A): 2.841500 64.96250 60.29650 number of atom coordinates read : 4461 total number of charged atoms : 4302 net assigned charge : -5.499955 assigned positive charge : 670.7770 centred at (gu) : 94.78447 88.84721 87.57784 assigned negative charge : -676.2803 centred at (gu) : 94.58565 89.17972 88.07641 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 99339 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34346 grid for indexing accessible points = 1.400000 m= 32724 mr = 71643 m= 3757 mr = 23874 m= 112 mr = 2142 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 6242 time to turn everything in is 0.7900000 number of dielectric boundary points 38263 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 358 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 33156 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) : 0.5627658 object centre at (A) : 2.841500 64.96250 60.29650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3722000E-02 -2.1203438E-02 midg,1,midg; midg,igrid,midg 1.3145762E-02 -1.6705822E-02 1,midg,midg; igrid,midg,midg -9.9036703E-03 1.7059298E-02 gauss-seidel spectral radius is 0.9984317 estimated iterations to convergence 200 setup time was (sec) 1.080000 now iterating at: 11:37:24 rms-change max change #iterations 4.544046 161.4570 at 10iterations 2.013101 61.66576 at 20iterations 0.8968697 29.58527 at 30iterations 0.3961952 12.31942 at 40iterations 0.1765672 5.052200 at 50iterations 7.8656994E-02 2.103111 at 60iterations 3.5039298E-02 0.9405975 at 70iterations 1.5603047E-02 0.5091553 at 80iterations 6.9523621E-03 0.1962137 at 90iterations 3.1168845E-03 9.1472626E-02 at 100iterations 1.4106722E-03 4.2892456E-02 at 110iterations 6.4558652E-04 1.8403769E-02 at 120iterations finished qdiffx linear iterations at : 11:37:33 total time elapsed so far: 10.70000 # loops : 120 mean,max change (kT/e) : 6.4558652E-04 1.8403769E-02 energy calculations done at 10.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.86000 DelPhi exited at 11:37:34 10.865u 0.493s 0:11.73 96.7% 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 8 2011 at 11:37:34 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 = 4461 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.532446 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): -28.78800 34.47100 ymin,ymax (A): 34.51100 95.41400 zmin,zma (A): 31.42300 89.17000 x,y,z range (A): 63.25900 60.90300 57.74699 scale (grids/A): 2.532446 object centre (A): 2.841500 64.96250 60.29650 number of atom coordinates read : 4461 total number of charged atoms : 4302 net assigned charge : -5.499955 assigned positive charge : 670.7770 centred at (gu) : 97.17641 88.27041 86.36641 assigned negative charge : -676.2803 centred at (gu) : 96.87837 88.76944 87.11449 start vw surface at 0.1700000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 231046 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34346 grid for indexing accessible points = 1.400000 m= 112280 mr = 174044 m= 34147 mr = 92064 m= 6217 mr = 26958 m= 493 mr = 4522 m= 9 mr = 263 m= 0 mr = 2 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 20484 time to turn everything in is 2.000000 number of dielectric boundary points 86339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 34397 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) : 1.688297 object centre at (A) : 2.841500 64.96250 60.29650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4004321 -0.2524411 midg,1,midg; midg,igrid,midg 0.1837889 -0.2907967 1,midg,midg; igrid,midg,midg -0.1272650 0.1745065 gauss-seidel spectral radius is 0.9992275 estimated iterations to convergence 284 setup time was (sec) 2.330000 now iterating at: 11:37:37 rms-change max change #iterations 11.29984 262.3964 at 10iterations 6.543423 138.7172 at 20iterations 3.775367 92.34648 at 30iterations 2.171544 47.27096 at 40iterations 1.243386 23.99990 at 50iterations 0.7117413 14.07816 at 60iterations 0.4073918 6.621092 at 70iterations 0.2320935 4.057005 at 80iterations 0.1323867 2.362161 at 90iterations 7.5395249E-02 1.267490 at 100iterations 4.2953368E-02 0.7454519 at 110iterations 2.4505572E-02 0.3862886 at 120iterations 1.3966321E-02 0.2460744 at 130iterations 7.9628313E-03 0.1190443 at 140iterations 4.5683002E-03 7.9603314E-02 at 150iterations 2.6384282E-03 4.4029236E-02 at 160iterations 1.5430881E-03 2.5997162E-02 at 170iterations 9.1857981E-04 1.5340805E-02 at 180iterations finished qdiffx linear iterations at : 11:37:53 total time elapsed so far: 18.71000 # loops : 180 mean,max change (kT/e) : 9.1857981E-04 1.5340805E-02 energy calculations done at 18.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.89000 DelPhi exited at 11:37:54 18.896u 0.498s 0:19.78 97.9% 0+0k 0+0io 0pf+0w