Sat Oct 8 17:13:17 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 Sat Oct 8 2011 at 17:13:17 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3349 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: 0.5496032 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): 37.04700 97.42800 ymin,ymax (A): 14.59100 79.36500 zmin,zma (A): -22.99100 27.87200 x,y,z range (A): 60.38100 64.77400 50.86300 scale (grids/A): 0.5496032 object centre (A): 67.23750 46.97800 2.440500 number of atom coordinates read : 3349 total number of charged atoms : 3204 net assigned charge : -6.499980 assigned positive charge : 501.6826 centred at (gu) : 88.92350 90.58587 89.34462 assigned negative charge : -508.1838 centred at (gu) : 88.94221 90.55015 89.32388 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6645 nv = 96 ne = 84 npr = 67430 no. pairs analyzed = 67430 no. exposed pairs = 4166 no. arc points = 28687 no. surface atoms = 1416 nbur = 1933 mkacc time = 0.1400000 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 = 1.568000 m= 283 mr = 3590 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2961 ## 393 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8630 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.6008788E-10 -2.4790586E-10 midg,1,midg; midg,igrid,midg -6.7598743E-10 -1.8076972E-10 1,midg,midg; igrid,midg,midg -3.9337059E-10 -4.8695209E-10 gauss-seidel spectral radius is 0.9829556 estimated iterations to convergence 63 setup time was (sec) 0.5700000 now iterating at: 17:13:18 rms-change max change #iterations 8.1467971E-02 14.80377 at 10iterations 5.5455770E-03 0.9087448 at 20iterations 4.2535379E-04 7.3440552E-02 at 30iterations 5.6505625E-05 1.0112762E-02 at 40iterations 1.3283619E-05 2.5882721E-03 at 50iterations finished qdiffx linear iterations at : 17:13:20 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 1.3283619E-05 2.5882721E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 17:13:21 3.211u 0.170s 0:03.66 92.3% 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 Sat Oct 8 2011 at 17:13:21 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3349 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: 1.648810 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): 37.04700 97.42800 ymin,ymax (A): 14.59100 79.36500 zmin,zma (A): -22.99100 27.87200 x,y,z range (A): 60.38100 64.77400 50.86300 scale (grids/A): 1.648810 object centre (A): 67.23750 46.97800 2.440500 number of atom coordinates read : 3349 total number of charged atoms : 3204 net assigned charge : -6.499980 assigned positive charge : 501.6826 centred at (gu) : 86.76955 91.75649 88.03288 assigned negative charge : -508.1838 centred at (gu) : 86.82638 91.64986 87.97118 start vw surface at 0.2000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 73820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28687 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23508 mr = 51481 m= 2436 mr = 16365 m= 89 mr = 1215 m= 0 mr = 5 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 532 time to turn everything in is 0.5600000 number of dielectric boundary points 30787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 327 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 24575 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) : 0.5496032 object centre at (A) : 67.23750 46.97800 2.440500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4934573E-03 -7.0048748E-03 midg,1,midg; midg,igrid,midg 2.7737829E-03 1.1901803E-02 1,midg,midg; igrid,midg,midg -2.0878736E-02 -4.1638934E-03 gauss-seidel spectral radius is 0.9982543 estimated iterations to convergence 190 setup time was (sec) 0.8300000 now iterating at: 17:13:22 rms-change max change #iterations 3.645460 159.8350 at 10iterations 1.546436 63.96296 at 20iterations 0.6552320 23.96924 at 30iterations 0.2787093 9.718657 at 40iterations 0.1187021 4.205919 at 50iterations 5.0254840E-02 1.719061 at 60iterations 2.1349652E-02 0.7038879 at 70iterations 9.1103893E-03 0.3209076 at 80iterations 3.8662669E-03 0.1219416 at 90iterations 1.6553723E-03 5.8506012E-02 at 100iterations 7.1463996E-04 2.5789261E-02 at 110iterations 3.1092181E-04 1.1312723E-02 at 120iterations finished qdiffx linear iterations at : 17:13:28 total time elapsed so far: 6.870000 # loops : 120 mean,max change (kT/e) : 3.1092181E-04 1.1312723E-02 energy calculations done at 6.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 17:13:28 7.051u 0.199s 0:07.52 96.2% 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 17:13:28 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3349 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.473214 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): 37.04700 97.42800 ymin,ymax (A): 14.59100 79.36500 zmin,zma (A): -22.99100 27.87200 x,y,z range (A): 60.38100 64.77400 50.86300 scale (grids/A): 2.473214 object centre (A): 67.23750 46.97800 2.440500 number of atom coordinates read : 3349 total number of charged atoms : 3204 net assigned charge : -6.499980 assigned positive charge : 501.6826 centred at (gu) : 85.15424 92.63422 87.04935 assigned negative charge : -508.1838 centred at (gu) : 85.23947 92.47465 86.95670 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 171204 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28687 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 81765 mr = 125331 m= 23544 mr = 65470 m= 3987 mr = 17790 m= 344 mr = 2660 m= 9 mr = 165 m= 0 mr = 2 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 1752 time to turn everything in is 1.250000 number of dielectric boundary points 69435 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 25593 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) : 1.648810 object centre at (A) : 67.23750 46.97800 2.440500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7662977E-02 -7.7948779E-02 midg,1,midg; midg,igrid,midg 0.1181652 0.3501402 1,midg,midg; igrid,midg,midg -0.2446967 -3.8919777E-02 gauss-seidel spectral radius is 0.9991664 estimated iterations to convergence 274 setup time was (sec) 1.550000 now iterating at: 17:13:30 rms-change max change #iterations 9.365032 356.0903 at 10iterations 5.302389 127.0503 at 20iterations 2.985776 72.28833 at 30iterations 1.674159 34.51619 at 40iterations 0.9372436 18.90428 at 50iterations 0.5245584 10.25200 at 60iterations 0.2926385 5.779720 at 70iterations 0.1630484 3.167863 at 80iterations 9.0676226E-02 1.843633 at 90iterations 5.0393473E-02 0.9719124 at 100iterations 2.8031442E-02 0.5869727 at 110iterations 1.5616550E-02 0.3186646 at 120iterations 8.6763147E-03 0.2000809 at 130iterations 4.8325639E-03 9.1357708E-02 at 140iterations 2.6927202E-03 5.5170059E-02 at 150iterations 1.5068222E-03 2.7381897E-02 at 160iterations 8.4968185E-04 1.7411232E-02 at 170iterations 4.8444857E-04 9.0777874E-03 at 180iterations finished qdiffx linear iterations at : 17:13:40 total time elapsed so far: 11.20000 # loops : 180 mean,max change (kT/e) : 4.8444857E-04 9.0777874E-03 energy calculations done at 11.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.37000 DelPhi exited at 17:13:40 11.373u 0.237s 0:11.88 97.6% 0+0k 0+0io 0pf+0w