Tue Nov 22 14:10:54 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 Tue Nov 22 2011 at 14:10:55 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 = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6255271 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): -35.31800 10.55900 ymin,ymax (A): 1.090000 42.62000 zmin,zma (A): -0.2760000 56.63600 x,y,z range (A): 45.87700 41.53000 56.91200 scale (grids/A): 0.6255271 object centre (A): -12.37950 21.85500 28.18000 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000007 assigned positive charge : 287.8720 centred at (gu) : 90.28183 89.21556 89.83855 assigned negative charge : -282.8723 centred at (gu) : 90.22850 89.30522 89.85554 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5238 nv = 96 ne = 84 npr = 40209 no. pairs analyzed = 40209 no. exposed pairs = 2411 no. arc points = 16960 no. surface atoms = 821 nbur = 1145 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 261 mr = 2899 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1695 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6193 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8662062E-09 3.6143886E-09 midg,1,midg; midg,igrid,midg 1.1565466E-08 -3.3234526E-10 1,midg,midg; igrid,midg,midg 1.5712140E-09 8.2000167E-09 gauss-seidel spectral radius is 0.9867083 estimated iterations to convergence 71 setup time was (sec) 0.4600000 now iterating at: 14:10:56 rms-change max change #iterations 0.1083518 17.43324 at 10iterations 1.0234590E-02 1.633497 at 20iterations 9.4311661E-04 0.1455841 at 30iterations 9.1198912E-05 1.6884327E-02 at 40iterations 8.4097601E-06 1.3694763E-03 at 50iterations finished qdiffx linear iterations at : 14:11:06 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 8.4097601E-06 1.3694763E-03 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 14:11:08 3.226u 0.178s 0:13.50 25.1% 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 Tue Nov 22 2011 at 14:11:12 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 = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.876581 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): -35.31800 10.55900 ymin,ymax (A): 1.090000 42.62000 zmin,zma (A): -0.2760000 56.63600 x,y,z range (A): 45.87700 41.53000 56.91200 scale (grids/A): 1.876581 object centre (A): -12.37950 21.85500 28.18000 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000007 assigned positive charge : 287.8720 centred at (gu) : 90.84549 87.64661 89.51574 assigned negative charge : -282.8723 centred at (gu) : 90.68575 87.91596 89.56681 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 56262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16960 grid for indexing accessible points = 1.400000 m= 20816 mr = 38857 m= 3358 mr = 15799 m= 182 mr = 2187 m= 4 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 155 time to turn everything in is 0.4000000 number of dielectric boundary points 23691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 100 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 14369 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) : 0.6255271 object centre at (A) : -12.37950 21.85500 28.18000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4649445E-02 3.2019444E-02 midg,1,midg; midg,igrid,midg 5.9861047E-03 1.2039125E-03 1,midg,midg; igrid,midg,midg -1.8309165E-03 -3.2548241E-03 gauss-seidel spectral radius is 0.9985198 estimated iterations to convergence 206 setup time was (sec) 0.6600000 now iterating at: 14:11:13 rms-change max change #iterations 3.441015 168.1332 at 10iterations 1.566488 60.48799 at 20iterations 0.7074217 26.95156 at 30iterations 0.3219638 11.44267 at 40iterations 0.1460999 5.708733 at 50iterations 6.6072151E-02 2.350822 at 60iterations 3.0124342E-02 1.048728 at 70iterations 1.3598536E-02 0.4988480 at 80iterations 6.1931671E-03 0.2142868 at 90iterations 2.8054330E-03 0.1013203 at 100iterations 1.2764185E-03 4.5406342E-02 at 110iterations 5.7561300E-04 2.3046494E-02 at 120iterations finished qdiffx linear iterations at : 14:11:30 total time elapsed so far: 6.650000 # loops : 120 mean,max change (kT/e) : 5.7561300E-04 2.3046494E-02 energy calculations done at 6.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.820000 DelPhi exited at 14:11:34 6.826u 0.160s 0:21.77 32.0% 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 Tue Nov 22 2011 at 14:11:36 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 = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.814872 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): -35.31800 10.55900 ymin,ymax (A): 1.090000 42.62000 zmin,zma (A): -0.2760000 56.63600 x,y,z range (A): 45.87700 41.53000 56.91200 scale (grids/A): 2.814872 object centre (A): -12.37950 21.85500 28.18000 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000007 assigned positive charge : 287.8720 centred at (gu) : 91.26814 86.46982 89.27360 assigned negative charge : -282.8723 centred at (gu) : 91.02871 86.87408 89.35033 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 130034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16960 grid for indexing accessible points = 1.400000 m= 66971 mr = 93943 m= 25136 mr = 55516 m= 5887 mr = 20784 m= 712 mr = 4560 m= 66 mr = 518 m= 0 mr = 44 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 511 time to turn everything in is 0.9800000 number of dielectric boundary points 53441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 14672 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) : 1.876581 object centre at (A) : -12.37950 21.85500 28.18000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1058195 0.2190009 midg,1,midg; midg,igrid,midg -2.2795131E-02 5.7870401E-03 1,midg,midg; igrid,midg,midg -5.2819565E-02 -7.7699102E-02 gauss-seidel spectral radius is 0.9992101 estimated iterations to convergence 281 setup time was (sec) 1.270000 now iterating at: 14:11:42 rms-change max change #iterations 8.225208 352.6925 at 10iterations 4.718050 119.7693 at 20iterations 2.671933 63.15718 at 30iterations 1.515519 36.39248 at 40iterations 0.8595148 16.92255 at 50iterations 0.4839085 11.65175 at 60iterations 0.2729493 5.816733 at 70iterations 0.1543241 3.308848 at 80iterations 8.6917199E-02 1.814934 at 90iterations 4.9024727E-02 0.9756012 at 100iterations 2.7622228E-02 0.5899963 at 110iterations 1.5544620E-02 0.3549764 at 120iterations 8.7728295E-03 0.1817856 at 130iterations 4.9330490E-03 0.1015739 at 140iterations 2.7816941E-03 5.7565689E-02 at 150iterations 1.5630450E-03 3.2809258E-02 at 160iterations 8.8068069E-04 1.7943859E-02 at 170iterations 4.9672055E-04 9.6397400E-03 at 180iterations finished qdiffx linear iterations at : 14:12:09 total time elapsed so far: 10.51000 # loops : 180 mean,max change (kT/e) : 4.9672055E-04 9.6397400E-03 energy calculations done at 10.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.69000 DelPhi exited at 14:12:12 10.690u 0.159s 0:37.24 29.1% 0+0k 0+0io 0pf+0w