Sat Oct 8 13:42:45 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 13:42:45 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3003 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: GLU 313 has a net charge of -0.2720 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 0.6397700 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): -12.21800 43.42700 ymin,ymax (A): -22.89900 22.44100 zmin,zma (A): -6.555000 47.83300 x,y,z range (A): 55.64500 45.34000 54.38800 scale (grids/A): 0.6397700 object centre (A): 15.60450 -0.2290001 20.63900 number of atom coordinates read : 3003 total number of charged atoms : 2858 net assigned charge : 0.7420080 assigned positive charge : 451.9127 centred at (gu) : 88.79733 89.75434 91.24361 assigned negative charge : -451.1713 centred at (gu) : 88.72639 89.59963 91.25347 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8132 nv = 96 ne = 84 npr = 62956 no. pairs analyzed = 62956 no. exposed pairs = 3377 no. arc points = 23787 no. surface atoms = 1149 nbur = 1854 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 395 mr = 4748 m= 4 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2300000 number of dielectric boundary points 3730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2296 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9900 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0115614E-09 -5.9990755E-11 midg,1,midg; midg,igrid,midg -2.0937238E-08 2.0597904E-08 1,midg,midg; igrid,midg,midg -1.0843586E-08 8.2952605E-09 gauss-seidel spectral radius is 0.9873726 estimated iterations to convergence 73 setup time was (sec) 0.4500000 now iterating at: 13:42:46 rms-change max change #iterations 0.1563494 22.62158 at 10iterations 1.5578909E-02 2.239708 at 20iterations 1.5955068E-03 0.2094841 at 30iterations 1.6392820E-04 2.3040771E-02 at 40iterations 1.7889362E-05 2.3345947E-03 at 50iterations finished qdiffx linear iterations at : 13:42:49 total time elapsed so far: 3.750000 # loops : 50 mean,max change (kT/e) : 1.7889362E-05 2.3345947E-03 energy calculations done at 3.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.880000 DelPhi exited at 13:42:50 3.882u 0.234s 0:04.43 92.7% 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 13:42:50 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3003 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: GLU 313 has a net charge of -0.2720 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 1.919310 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): -12.21800 43.42700 ymin,ymax (A): -22.89900 22.44100 zmin,zma (A): -6.555000 47.83300 x,y,z range (A): 55.64500 45.34000 54.38800 scale (grids/A): 1.919310 object centre (A): 15.60450 -0.2290001 20.63900 number of atom coordinates read : 3003 total number of charged atoms : 2858 net assigned charge : 0.7420080 assigned positive charge : 451.9127 centred at (gu) : 86.39146 89.26289 93.73014 assigned negative charge : -451.1713 centred at (gu) : 86.17878 88.79867 93.76000 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 88533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23787 grid for indexing accessible points = 1.400000 m= 31300 mr = 63796 m= 4593 mr = 23614 m= 306 mr = 2812 m= 6 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 194 time to turn everything in is 0.4300000 number of dielectric boundary points 34380 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 22509 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) : 0.6397700 object centre at (A) : 15.60450 -0.2290001 20.63900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7193881E-03 4.4979821E-03 midg,1,midg; midg,igrid,midg -5.3772014E-03 2.9908912E-02 1,midg,midg; igrid,midg,midg -3.6216833E-02 1.6457090E-02 gauss-seidel spectral radius is 0.9986879 estimated iterations to convergence 219 setup time was (sec) 0.6800000 now iterating at: 13:42:51 rms-change max change #iterations 4.698496 168.7302 at 10iterations 2.238256 65.41489 at 20iterations 1.066647 32.72030 at 30iterations 0.5083780 15.13990 at 40iterations 0.2413573 7.057533 at 50iterations 0.1147087 3.537987 at 60iterations 5.4824177E-02 1.624790 at 70iterations 2.6075488E-02 0.7514162 at 80iterations 1.2432147E-02 0.3895168 at 90iterations 5.8990871E-03 0.1586990 at 100iterations 2.8106743E-03 8.7005615E-02 at 110iterations 1.3424492E-03 4.0723801E-02 at 120iterations finished qdiffx linear iterations at : 13:42:59 total time elapsed so far: 8.620000 # loops : 120 mean,max change (kT/e) : 1.3424492E-03 4.0723801E-02 energy calculations done at 8.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.760000 DelPhi exited at 13:42:59 8.760u 0.271s 0:09.36 96.4% 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 13:42:59 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3003 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: GLU 313 has a net charge of -0.2720 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 2.878965 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): -12.21800 43.42700 ymin,ymax (A): -22.89900 22.44100 zmin,zma (A): -6.555000 47.83300 x,y,z range (A): 55.64500 45.34000 54.38800 scale (grids/A): 2.878965 object centre (A): 15.60450 -0.2290001 20.63900 number of atom coordinates read : 3003 total number of charged atoms : 2858 net assigned charge : 0.7420080 assigned positive charge : 451.9127 centred at (gu) : 84.58707 88.89426 95.59512 assigned negative charge : -451.1713 centred at (gu) : 84.26826 88.19804 95.63994 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 205211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23787 grid for indexing accessible points = 1.400000 m= 103431 mr = 154023 m= 35419 mr = 86262 m= 8146 mr = 28662 m= 1297 mr = 6026 m= 100 mr = 904 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 673 time to turn everything in is 1.170000 number of dielectric boundary points 77673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 22863 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) : 1.919310 object centre at (A) : 15.60450 -0.2290001 20.63900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1200534E-02 0.1743319 midg,1,midg; midg,igrid,midg -3.9054781E-02 0.3045076 1,midg,midg; igrid,midg,midg -0.5838894 0.2093277 gauss-seidel spectral radius is 0.9992751 estimated iterations to convergence 293 setup time was (sec) 1.460000 now iterating at: 13:43:01 rms-change max change #iterations 10.91028 371.9983 at 10iterations 6.373001 126.0525 at 20iterations 3.699230 69.72162 at 30iterations 2.146656 37.38819 at 40iterations 1.243172 23.00629 at 50iterations 0.7211828 13.25908 at 60iterations 0.4163650 6.655273 at 70iterations 0.2410185 4.113692 at 80iterations 0.1395075 2.388292 at 90iterations 8.0613866E-02 1.304435 at 100iterations 4.6568118E-02 0.8160987 at 110iterations 2.6888292E-02 0.5036049 at 120iterations 1.5549104E-02 0.2652683 at 130iterations 8.9852484E-03 0.1476941 at 140iterations 5.1822118E-03 9.1475248E-02 at 150iterations 2.9896698E-03 4.8868179E-02 at 160iterations 1.7290860E-03 3.1663895E-02 at 170iterations 1.0002252E-03 1.6094208E-02 at 180iterations finished qdiffx linear iterations at : 13:43:13 total time elapsed so far: 13.99000 # loops : 180 mean,max change (kT/e) : 1.0002252E-03 1.6094208E-02 energy calculations done at 13.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.13000 DelPhi exited at 13:43:14 14.130u 0.241s 0:14.66 98.0% 0+0k 0+0io 0pf+0w