Mon Oct 10 17:00:30 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 Mon Oct 10 2011 at 17:00:30 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2687 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: 0.5769948 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): -31.14700 30.55200 ymin,ymax (A): -21.15700 25.60000 zmin,zma (A): -7.448000 39.72700 x,y,z range (A): 61.69900 46.75700 47.17500 scale (grids/A): 0.5769948 object centre (A): -0.2974997 2.221500 16.13950 number of atom coordinates read : 2687 total number of charged atoms : 2545 net assigned charge : -4.499967 assigned positive charge : 398.2736 centred at (gu) : 90.38107 90.32104 89.38115 assigned negative charge : -402.7744 centred at (gu) : 90.44965 90.09813 89.32379 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5853 nv = 96 ne = 84 npr = 53732 no. pairs analyzed = 53732 no. exposed pairs = 3492 no. arc points = 24597 no. surface atoms = 1189 nbur = 1498 mkacc time = 9.9999994E-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= 229 mr = 3022 m= 0 mr = 4 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2465 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7513 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2251809E-09 1.2098055E-10 midg,1,midg; midg,igrid,midg -4.6463087E-09 3.2826553E-09 1,midg,midg; igrid,midg,midg 3.1248346E-10 -2.3292945E-09 gauss-seidel spectral radius is 0.9844773 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 17:00:30 rms-change max change #iterations 9.0522125E-02 15.38618 at 10iterations 6.9177384E-03 1.357392 at 20iterations 5.3611549E-04 8.3510399E-02 at 30iterations 4.1158204E-05 6.4315796E-03 at 40iterations 3.6752458E-06 6.2942505E-04 at 50iterations finished qdiffx linear iterations at : 17:00:33 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 3.6752458E-06 6.2942505E-04 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 17:00:34 3.398u 0.175s 0:04.19 84.9% 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 Mon Oct 10 2011 at 17:00:34 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2687 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: 1.730984 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): -31.14700 30.55200 ymin,ymax (A): -21.15700 25.60000 zmin,zma (A): -7.448000 39.72700 x,y,z range (A): 61.69900 46.75700 47.17500 scale (grids/A): 1.730984 object centre (A): -0.2974997 2.221500 16.13950 number of atom coordinates read : 2687 total number of charged atoms : 2545 net assigned charge : -4.499967 assigned positive charge : 398.2736 centred at (gu) : 91.14283 90.96242 88.14257 assigned negative charge : -402.7744 centred at (gu) : 91.34879 90.29414 87.97108 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64631 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24597 grid for indexing accessible points = 1.400000 m= 20207 mr = 43288 m= 2258 mr = 13977 m= 60 mr = 1195 m= 0 mr = 7 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 688 time to turn everything in is 0.3200000 number of dielectric boundary points 28689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 222 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 19830 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) : 0.5769948 object centre at (A) : -0.2974997 2.221500 16.13950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0817958E-03 -3.4681978E-03 midg,1,midg; midg,igrid,midg -2.5633689E-02 1.2771755E-02 1,midg,midg; igrid,midg,midg 8.2332501E-03 -1.7554611E-03 gauss-seidel spectral radius is 0.9983633 estimated iterations to convergence 196 setup time was (sec) 0.5300000 now iterating at: 17:00:35 rms-change max change #iterations 3.539195 149.2081 at 10iterations 1.530693 61.05922 at 20iterations 0.6660352 23.31007 at 30iterations 0.2912113 10.50891 at 40iterations 0.1264691 4.487377 at 50iterations 5.5114131E-02 2.143572 at 60iterations 2.3974808E-02 0.8857379 at 70iterations 1.0425206E-02 0.3701793 at 80iterations 4.5560873E-03 0.2191842 at 90iterations 1.9912941E-03 7.1014404E-02 at 100iterations 8.6259085E-04 3.1374931E-02 at 110iterations 3.7676259E-04 1.2350082E-02 at 120iterations finished qdiffx linear iterations at : 17:00:42 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 3.7676259E-04 1.2350082E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 17:00:43 7.702u 0.199s 0:09.29 84.9% 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 Mon Oct 10 2011 at 17:00:43 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2687 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: 2.596477 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): -31.14700 30.55200 ymin,ymax (A): -21.15700 25.60000 zmin,zma (A): -7.448000 39.72700 x,y,z range (A): 61.69900 46.75700 47.17500 scale (grids/A): 2.596477 object centre (A): -0.2974997 2.221500 16.13950 number of atom coordinates read : 2687 total number of charged atoms : 2545 net assigned charge : -4.499967 assigned positive charge : 398.2736 centred at (gu) : 91.71407 91.44354 87.21370 assigned negative charge : -402.7744 centred at (gu) : 92.02293 90.44109 86.95657 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 150269 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24597 grid for indexing accessible points = 1.400000 m= 68825 mr = 106344 m= 20574 mr = 54116 m= 3541 mr = 15752 m= 282 mr = 2394 m= 6 mr = 146 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 2434 time to turn everything in is 0.7800000 number of dielectric boundary points 64745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20352 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) : 1.730984 object centre at (A) : -0.2974997 2.221500 16.13950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9192845E-02 -5.2353971E-02 midg,1,midg; midg,igrid,midg -0.2947826 0.1906113 1,midg,midg; igrid,midg,midg 0.3774981 5.3941570E-02 gauss-seidel spectral radius is 0.9991915 estimated iterations to convergence 278 setup time was (sec) 1.000000 now iterating at: 17:00:45 rms-change max change #iterations 8.961714 326.8707 at 10iterations 5.136771 137.3041 at 20iterations 2.917171 69.51514 at 30iterations 1.651588 42.22955 at 40iterations 0.9349322 24.72774 at 50iterations 0.5272282 12.13350 at 60iterations 0.2959586 6.774281 at 70iterations 0.1664288 4.088267 at 80iterations 9.3500704E-02 1.973368 at 90iterations 5.2436255E-02 1.053858 at 100iterations 2.9386446E-02 0.5579138 at 110iterations 1.6416261E-02 0.3302956 at 120iterations 9.2170713E-03 0.1864758 at 130iterations 5.1557305E-03 0.1123600 at 140iterations 2.8984705E-03 6.0108185E-02 at 150iterations 1.6179072E-03 3.4742355E-02 at 160iterations 9.0366357E-04 1.8362045E-02 at 170iterations 5.0605007E-04 1.0225296E-02 at 180iterations finished qdiffx linear iterations at : 17:00:55 total time elapsed so far: 11.85000 # loops : 180 mean,max change (kT/e) : 5.0605007E-04 1.0225296E-02 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.98000 DelPhi exited at 17:00:56 11.985u 0.196s 0:12.78 95.2% 0+0k 0+0io 0pf+0w