Sun Oct 9 16:57:58 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 Sun Oct 9 2011 at 16:57:58 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 = 5605 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 : 5450 net assigned charge : 13.50003 assigned positive charge : 847.3890 centred at (gu) : 90.04565 90.68208 90.53322 assigned negative charge : -833.8956 centred at (gu) : 90.12599 90.78312 90.40712 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 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 = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 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 0.4400000 number of grid points assigned charge 10676 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0688761E-11 1.4752573E-10 midg,1,midg; midg,igrid,midg 9.1119029E-11 -3.6462545E-11 1,midg,midg; igrid,midg,midg 9.5012033E-11 -1.5195642E-11 gauss-seidel spectral radius is 0.9777034 estimated iterations to convergence 56 setup time was (sec) 0.5600000 now iterating at: 16:57:58 rms-change max change #iterations 5.4553926E-02 8.770483 at 10iterations 5.9498157E-03 1.253059 at 20iterations 2.6360566E-03 0.5953026 at 30iterations 1.2902733E-03 0.2894897 at 40iterations 6.3173106E-04 0.1413765 at 50iterations finished qdiffx linear iterations at : 16:58:01 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 6.3173106E-04 0.1413765 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 16:58:02 3.649u 0.171s 0:04.10 92.9% 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 Sun Oct 9 2011 at 16:58:02 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 = 5605 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 : 5450 net assigned charge : 13.50003 assigned positive charge : 847.3890 centred at (gu) : 90.13525 92.04463 91.59792 assigned negative charge : -833.8956 centred at (gu) : 90.37764 92.34904 91.22117 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 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 = 0.1800000 no. cavity mid-points inaccessible to solvent = 488 time to turn everything in is 0.4400000 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 0.5200000 number of grid points assigned charge 39920 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 -1.2220071E-02 2.9793696E-02 midg,1,midg; midg,igrid,midg 8.5567450E-03 -1.4961426E-03 1,midg,midg; igrid,midg,midg 1.5282148E-02 3.9221253E-03 gauss-seidel spectral radius is 0.9978667 estimated iterations to convergence 172 setup time was (sec) 0.6700000 now iterating at: 16:58:03 rms-change max change #iterations 3.524295 147.5816 at 10iterations 1.367723 48.39935 at 20iterations 0.5296647 17.36570 at 30iterations 0.2067952 6.600517 at 40iterations 8.0817923E-02 2.664349 at 50iterations 3.2523222E-02 1.039743 at 60iterations 1.3983451E-02 0.4872208 at 70iterations 7.1904687E-03 0.3203926 at 80iterations 4.5357780E-03 0.1957855 at 90iterations 3.2550881E-03 0.1423416 at 100iterations 2.4453423E-03 0.1056976 at 110iterations 1.8619169E-03 7.8834534E-02 at 120iterations finished qdiffx linear iterations at : 16:58:10 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.8619169E-03 7.8834534E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 16:58:10 8.032u 0.194s 0:08.53 96.3% 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 16:58:10 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 = 5605 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 : 5450 net assigned charge : 13.50003 assigned positive charge : 847.3890 centred at (gu) : 90.20225 93.06672 92.39655 assigned negative charge : -833.8956 centred at (gu) : 90.56643 93.52341 91.83157 start vw surface at 0.1400000 fill in re-entrant regions at 0.3800000 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 = 0.5900000 no. cavity mid-points inaccessible to solvent = 1637 time to turn everything in is 1.060000 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 1.160000 number of grid points assigned charge 43363 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 -0.2728322 0.6048542 midg,1,midg; midg,igrid,midg 0.1489828 -3.5134446E-02 1,midg,midg; igrid,midg,midg 0.2874390 9.3041971E-02 gauss-seidel spectral radius is 0.9990977 estimated iterations to convergence 263 setup time was (sec) 1.310000 now iterating at: 16:58:12 rms-change max change #iterations 10.03720 274.6079 at 10iterations 5.660368 161.5036 at 20iterations 3.165515 75.44325 at 30iterations 1.760165 43.44888 at 40iterations 0.9731876 22.73932 at 50iterations 0.5364026 11.22100 at 60iterations 0.2943798 6.127978 at 70iterations 0.1613997 3.407593 at 80iterations 8.8389866E-02 1.799290 at 90iterations 4.8368841E-02 1.013126 at 100iterations 2.6561152E-02 0.5984192 at 110iterations 1.4626054E-02 0.2871590 at 120iterations 8.1859017E-03 0.1682320 at 130iterations 4.7198492E-03 0.1130028 at 140iterations 2.8681306E-03 7.5008392E-02 at 150iterations 1.8982630E-03 4.9087524E-02 at 160iterations 1.3747042E-03 3.4606934E-02 at 170iterations 1.0602351E-03 2.7221680E-02 at 180iterations finished qdiffx linear iterations at : 16:58:24 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 1.0602351E-03 2.7221680E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 16:58:24 13.009u 0.191s 0:13.46 97.9% 0+0k 0+0io 0pf+0w