Sun Oct 9 16:58:24 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+sph2.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 = amb2.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 Sun Oct 9 2011 at 16:58:24 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5605 !!! WARNING: GLM 285 has a net charge of -0.0940 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: 0.4782504 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): 3.206000 67.50700 ymin,ymax (A): -0.7670000 54.60400 zmin,zma (A): -42.11700 32.32100 x,y,z range (A): 64.30099 55.37100 74.43800 scale (grids/A): 0.4782504 object centre (A): 35.35650 26.91850 -4.897999 number of atom coordinates read : 5605 total number of charged atoms : 5446 net assigned charge : 13.40606 assigned positive charge : 847.8290 centred at (gu) : 90.04567 90.68624 90.53497 assigned negative charge : -834.4296 centred at (gu) : 90.12576 90.78645 90.40945 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7724 nv = 96 ne = 84 npr = 115922 no. pairs analyzed = 115922 no. exposed pairs = 6415 no. arc points = 43649 no. surface atoms = 2186 nbur = 3419 mkacc time = 0.2000000 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 = 1.764000 m= 226 mr = 4136 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4237 ## 752 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 10675 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0608673E-11 1.4687672E-10 midg,1,midg; midg,igrid,midg 9.0349367E-11 -3.6190464E-11 1,midg,midg; igrid,midg,midg 9.4592355E-11 -1.5343015E-11 gauss-seidel spectral radius is 0.9777034 estimated iterations to convergence 56 setup time was (sec) 0.5700000 now iterating at: 16:58:25 rms-change max change #iterations 5.4877352E-02 8.845057 at 10iterations 5.9989151E-03 1.256622 at 20iterations 2.6548828E-03 0.5981522 at 30iterations 1.2987957E-03 0.2910461 at 40iterations 6.3574698E-04 0.1422081 at 50iterations finished qdiffx linear iterations at : 16:58:28 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 6.3574698E-04 0.1422081 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 16:58:28 3.628u 0.164s 0:04.06 93.1% 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 Sun Oct 9 2011 at 16:58:28 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5605 !!! WARNING: GLM 285 has a net charge of -0.0940 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: 1.434751 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): 3.206000 67.50700 ymin,ymax (A): -0.7670000 54.60400 zmin,zma (A): -42.11700 32.32100 x,y,z range (A): 64.30099 55.37100 74.43800 scale (grids/A): 1.434751 object centre (A): 35.35650 26.91850 -4.897999 number of atom coordinates read : 5605 total number of charged atoms : 5446 net assigned charge : 13.40606 assigned positive charge : 847.8290 centred at (gu) : 90.13535 92.05710 91.60319 assigned negative charge : -834.4296 centred at (gu) : 90.37695 92.35901 91.22820 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 90099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43649 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 23093 mr = 63627 m= 1428 mr = 14976 m= 13 mr = 545 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 488 time to turn everything in is 0.4500000 number of dielectric boundary points 35485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 837 ## 24 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 39892 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) : 0.4782504 object centre at (A) : 35.35650 26.91850 -4.897999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2237639E-02 2.9672330E-02 midg,1,midg; midg,igrid,midg 8.4862038E-03 -1.3793437E-03 1,midg,midg; igrid,midg,midg 1.5185855E-02 3.9007557E-03 gauss-seidel spectral radius is 0.9978667 estimated iterations to convergence 172 setup time was (sec) 0.6700000 now iterating at: 16:58:29 rms-change max change #iterations 3.528129 147.5815 at 10iterations 1.369263 48.39935 at 20iterations 0.5302963 17.76909 at 30iterations 0.2070518 6.681046 at 40iterations 8.0944180E-02 2.723728 at 50iterations 3.2584623E-02 1.044535 at 60iterations 1.4033576E-02 0.4852600 at 70iterations 7.2335736E-03 0.3217621 at 80iterations 4.5691156E-03 0.1965103 at 90iterations 3.2808147E-03 0.1429596 at 100iterations 2.4644269E-03 0.1062469 at 110iterations 1.8761093E-03 7.9322815E-02 at 120iterations finished qdiffx linear iterations at : 16:58:36 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 1.8761093E-03 7.9322815E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 16:58:37 7.948u 0.178s 0:08.49 95.5% 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 Sun Oct 9 2011 at 16:58:37 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5605 !!! WARNING: GLM 285 has a net charge of -0.0940 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: 2.152127 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): 3.206000 67.50700 ymin,ymax (A): -0.7670000 54.60400 zmin,zma (A): -42.11700 32.32100 x,y,z range (A): 64.30099 55.37100 74.43800 scale (grids/A): 2.152127 object centre (A): 35.35650 26.91850 -4.897999 number of atom coordinates read : 5605 total number of charged atoms : 5446 net assigned charge : 13.40606 assigned positive charge : 847.8290 centred at (gu) : 90.20241 93.08540 92.40444 assigned negative charge : -834.4296 centred at (gu) : 90.56539 93.53836 91.84212 start vw surface at 0.1300000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 211367 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43649 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 87660 mr = 156843 m= 18437 mr = 68190 m= 1876 mr = 13019 m= 52 mr = 1067 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 1637 time to turn everything in is 1.020000 number of dielectric boundary points 80261 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 43331 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) : 1.434751 object centre at (A) : 35.35650 26.91850 -4.897999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2731842 0.6021686 midg,1,midg; midg,igrid,midg 0.1476573 -3.2410808E-02 1,midg,midg; igrid,midg,midg 0.2855698 9.2626594E-02 gauss-seidel spectral radius is 0.9990977 estimated iterations to convergence 263 setup time was (sec) 1.270000 now iterating at: 16:58:38 rms-change max change #iterations 10.04833 274.5999 at 10iterations 5.666682 161.5059 at 20iterations 3.168107 75.44449 at 30iterations 1.761739 43.00211 at 40iterations 0.9739289 22.84900 at 50iterations 0.5368272 11.22101 at 60iterations 0.2946117 6.096359 at 70iterations 0.1615254 3.459824 at 80iterations 8.8453628E-02 1.806702 at 90iterations 4.8410088E-02 1.016602 at 100iterations 2.6585110E-02 0.6000824 at 110iterations 1.4644022E-02 0.2868042 at 120iterations 8.2003595E-03 0.1667442 at 130iterations 4.7329213E-03 0.1133499 at 140iterations 2.8809067E-03 7.5279236E-02 at 150iterations 1.9104440E-03 4.9438477E-02 at 160iterations 1.3859273E-03 3.4927368E-02 at 170iterations 1.0699731E-03 2.7381897E-02 at 180iterations finished qdiffx linear iterations at : 16:58:50 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 1.0699731E-03 2.7381897E-02 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 16:58:50 12.965u 0.202s 0:13.44 97.9% 0+0k 0+0io 0pf+0w