Sat Oct 8 11:38:17 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 11:38:18 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2669 !!! WARNING: ASL 92 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5761916 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): -37.49600 19.20800 ymin,ymax (A): -27.30700 34.47800 zmin,zma (A): -7.298000 44.29600 x,y,z range (A): 56.70400 61.78500 51.59400 scale (grids/A): 0.5761916 object centre (A): -9.143999 3.585500 18.49900 number of atom coordinates read : 2669 total number of charged atoms : 2519 net assigned charge : 0.4000052 assigned positive charge : 391.1686 centred at (gu) : 91.03768 89.58425 88.97511 assigned negative charge : -390.7693 centred at (gu) : 91.07301 89.49702 89.00172 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5898 nv = 96 ne = 84 npr = 52475 no. pairs analyzed = 52475 no. exposed pairs = 3583 no. arc points = 25747 no. surface atoms = 1215 nbur = 1454 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 = 1.484000 m= 216 mr = 2848 m= 0 mr = 7 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3259 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2555 ## 288 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 7405 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8664507E-10 -2.8772063E-10 midg,1,midg; midg,igrid,midg -1.5623466E-09 1.4071663E-09 1,midg,midg; igrid,midg,midg 5.3497601E-10 -6.6614991E-10 gauss-seidel spectral radius is 0.9844402 estimated iterations to convergence 66 setup time was (sec) 0.8200000 now iterating at: 11:38:19 rms-change max change #iterations 9.0248682E-02 15.01463 at 10iterations 6.7040981E-03 1.131792 at 20iterations 5.1374495E-04 7.7028275E-02 at 30iterations 4.0066017E-05 6.5317154E-03 at 40iterations 3.4143848E-06 6.2912703E-04 at 50iterations finished qdiffx linear iterations at : 11:38:25 total time elapsed so far: 6.980000 # loops : 50 mean,max change (kT/e) : 3.4143848E-06 6.2912703E-04 energy calculations done at 6.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.180000 DelPhi exited at 11:38:26 7.184u 0.723s 0:08.34 94.7% 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 11:38:26 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2669 !!! WARNING: ASL 92 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.728575 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): -37.49600 19.20800 ymin,ymax (A): -27.30700 34.47800 zmin,zma (A): -7.298000 44.29600 x,y,z range (A): 56.70400 61.78500 51.59400 scale (grids/A): 1.728575 object centre (A): -9.143999 3.585500 18.49900 number of atom coordinates read : 2669 total number of charged atoms : 2519 net assigned charge : 0.4000052 assigned positive charge : 391.1686 centred at (gu) : 93.11263 88.75178 86.92471 assigned negative charge : -390.7693 centred at (gu) : 93.21867 88.49059 87.00476 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 64392 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25747 grid for indexing accessible points = 1.400000 m= 19351 mr = 41618 m= 2138 mr = 13185 m= 72 mr = 983 m= 0 mr = 9 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 174 time to turn everything in is 0.6600000 number of dielectric boundary points 30158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 226 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 19516 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) : 0.5761916 object centre at (A) : -9.143999 3.585500 18.49900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7012023E-03 -1.1089784E-02 midg,1,midg; midg,igrid,midg -1.4023265E-02 -1.9108951E-04 1,midg,midg; igrid,midg,midg 1.3628259E-03 1.1489638E-02 gauss-seidel spectral radius is 0.9983701 estimated iterations to convergence 197 setup time was (sec) 1.190000 now iterating at: 11:38:28 rms-change max change #iterations 3.498075 177.5261 at 10iterations 1.518654 54.36687 at 20iterations 0.6598209 24.26454 at 30iterations 0.2867215 10.39204 at 40iterations 0.1256136 4.515939 at 50iterations 5.4480251E-02 2.154549 at 60iterations 2.3791144E-02 0.8749018 at 70iterations 1.0372151E-02 0.4014587 at 80iterations 4.5237807E-03 0.1757278 at 90iterations 1.9765203E-03 7.1166992E-02 at 100iterations 8.6204358E-04 3.2246590E-02 at 110iterations 3.7775142E-04 1.4701843E-02 at 120iterations finished qdiffx linear iterations at : 11:38:45 total time elapsed so far: 17.76000 # loops : 120 mean,max change (kT/e) : 3.7775142E-04 1.4701843E-02 energy calculations done at 17.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.93000 DelPhi exited at 11:38:45 17.934u 0.786s 0:19.05 98.2% 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 11:38:45 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2669 !!! WARNING: ASL 92 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.592862 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): -37.49600 19.20800 ymin,ymax (A): -27.30700 34.47800 zmin,zma (A): -7.298000 44.29600 x,y,z range (A): 56.70400 61.78500 51.59400 scale (grids/A): 2.592862 object centre (A): -9.143999 3.585500 18.49900 number of atom coordinates read : 2669 total number of charged atoms : 2519 net assigned charge : 0.4000052 assigned positive charge : 391.1686 centred at (gu) : 94.66887 88.12762 85.38688 assigned negative charge : -390.7693 centred at (gu) : 94.82810 87.73588 85.50718 start vw surface at 0.1200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 149066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25747 grid for indexing accessible points = 1.400000 m= 66049 mr = 102039 m= 19704 mr = 51364 m= 3274 mr = 14712 m= 274 mr = 2042 m= 5 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 569 time to turn everything in is 1.620000 number of dielectric boundary points 68088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 20140 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) : 1.728575 object centre at (A) : -9.143999 3.585500 18.49900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4740839E-02 -0.1707989 midg,1,midg; midg,igrid,midg -0.1956781 6.7802340E-02 1,midg,midg; igrid,midg,midg -1.5930187E-02 0.2041391 gauss-seidel spectral radius is 0.9991933 estimated iterations to convergence 278 setup time was (sec) 2.230000 now iterating at: 11:38:48 rms-change max change #iterations 8.835349 381.7243 at 10iterations 5.077162 152.5771 at 20iterations 2.908491 64.04693 at 30iterations 1.649058 42.32555 at 40iterations 0.9344136 21.44915 at 50iterations 0.5266010 11.59148 at 60iterations 0.2972042 6.373581 at 70iterations 0.1668808 3.298840 at 80iterations 9.4191343E-02 2.012978 at 90iterations 5.2776504E-02 1.088285 at 100iterations 2.9681662E-02 0.6244903 at 110iterations 1.6624613E-02 0.3900102 at 120iterations 9.3569895E-03 0.1990337 at 130iterations 5.2433959E-03 0.1044903 at 140iterations 2.9377725E-03 6.4482689E-02 at 150iterations 1.6510549E-03 3.1535625E-02 at 160iterations 9.2504139E-04 2.3330688E-02 at 170iterations 5.2009989E-04 1.0547638E-02 at 180iterations finished qdiffx linear iterations at : 11:39:18 total time elapsed so far: 32.23000 # loops : 180 mean,max change (kT/e) : 5.2009989E-04 1.0547638E-02 energy calculations done at 32.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 32.42000 DelPhi exited at 11:39:19 32.423u 0.825s 0:33.67 98.7% 0+0k 0+0io 0pf+0w