Tue Nov 22 14:10:35 PST 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 Tue Nov 22 2011 at 14:10:37 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6017172 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): -23.74500 35.41900 ymin,ymax (A): -18.71400 20.12300 zmin,zma (A): -2.820000 38.49800 x,y,z range (A): 59.16400 38.83700 41.31800 scale (grids/A): 0.6017172 object centre (A): 5.837002 0.7045002 17.83900 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 3.000004 assigned positive charge : 289.5139 centred at (gu) : 89.59763 90.29166 90.15270 assigned negative charge : -286.5143 centred at (gu) : 89.60893 90.37310 90.28543 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4699 nv = 96 ne = 84 npr = 40045 no. pairs analyzed = 40045 no. exposed pairs = 2431 no. arc points = 17161 no. surface atoms = 821 nbur = 1125 mkacc time = 7.0000008E-02 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 = 1.456000 m= 209 mr = 2549 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.1600000 number of dielectric boundary points 2350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1765 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 5819 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9168380E-09 -2.5452820E-09 midg,1,midg; midg,igrid,midg 3.4346641E-09 -1.0327521E-09 1,midg,midg; igrid,midg,midg 1.8550159E-09 9.6661024E-10 gauss-seidel spectral radius is 0.9856493 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 14:10:38 rms-change max change #iterations 9.5161453E-02 18.40950 at 10iterations 8.1836041E-03 1.360056 at 20iterations 6.9398398E-04 0.1476746 at 30iterations 5.8442452E-05 1.0239601E-02 at 40iterations 4.9738774E-06 8.3923340E-04 at 50iterations finished qdiffx linear iterations at : 14:10:44 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 4.9738774E-06 8.3923340E-04 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 14:10:45 3.740u 0.270s 0:08.32 48.1% 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 Tue Nov 22 2011 at 14:10:45 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.805152 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): -23.74500 35.41900 ymin,ymax (A): -18.71400 20.12300 zmin,zma (A): -2.820000 38.49800 x,y,z range (A): 59.16400 38.83700 41.31800 scale (grids/A): 1.805152 object centre (A): 5.837002 0.7045002 17.83900 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 3.000004 assigned positive charge : 289.5139 centred at (gu) : 88.79282 90.87509 90.45805 assigned negative charge : -286.5143 centred at (gu) : 88.82710 91.11944 90.85638 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 51473 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17161 grid for indexing accessible points = 1.400000 m= 17991 mr = 35139 m= 2324 mr = 13375 m= 76 mr = 1398 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 1139 time to turn everything in is 0.2700000 number of dielectric boundary points 21945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 14205 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) : 0.6017172 object centre at (A) : 5.837002 0.7045002 17.83900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3404325E-03 -5.4640402E-03 midg,1,midg; midg,igrid,midg 2.2646629E-03 -3.5538983E-03 1,midg,midg; igrid,midg,midg 3.9529566E-02 3.2819007E-02 gauss-seidel spectral radius is 0.9984035 estimated iterations to convergence 199 setup time was (sec) 0.5200000 now iterating at: 14:10:46 rms-change max change #iterations 3.212258 188.5780 at 10iterations 1.412344 59.02539 at 20iterations 0.6240351 23.54443 at 30iterations 0.2736611 10.52209 at 40iterations 0.1204375 4.721436 at 50iterations 5.2722413E-02 2.189519 at 60iterations 2.3276202E-02 0.8705293 at 70iterations 1.0234597E-02 0.4608383 at 80iterations 4.5008506E-03 0.1817608 at 90iterations 1.9790421E-03 7.5748444E-02 at 100iterations 8.7212818E-04 3.3897638E-02 at 110iterations 3.8406189E-04 1.4938354E-02 at 120iterations finished qdiffx linear iterations at : 14:10:59 total time elapsed so far: 8.930000 # loops : 120 mean,max change (kT/e) : 3.8406189E-04 1.4938354E-02 energy calculations done at 8.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.060000 DelPhi exited at 14:11:00 9.063u 0.369s 0:14.92 63.1% 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 Tue Nov 22 2011 at 14:11:00 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.707728 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): -23.74500 35.41900 ymin,ymax (A): -18.71400 20.12300 zmin,zma (A): -2.820000 38.49800 x,y,z range (A): 59.16400 38.83700 41.31800 scale (grids/A): 2.707728 object centre (A): 5.837002 0.7045002 17.83900 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 3.000004 assigned positive charge : 289.5139 centred at (gu) : 88.18918 91.31257 90.68703 assigned negative charge : -286.5143 centred at (gu) : 88.24067 91.67929 91.28461 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 118946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17161 grid for indexing accessible points = 1.400000 m= 59357 mr = 85147 m= 19867 mr = 48760 m= 3930 mr = 16105 m= 302 mr = 2841 m= 12 mr = 137 m= 0 mr = 2 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 3833 time to turn everything in is 0.6700000 number of dielectric boundary points 49422 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 14508 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) : 1.805152 object centre at (A) : 5.837002 0.7045002 17.83900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5432636E-02 -4.8883822E-02 midg,1,midg; midg,igrid,midg 1.4534853E-02 -3.4347579E-02 1,midg,midg; igrid,midg,midg 0.4477673 0.2958114 gauss-seidel spectral radius is 0.9991767 estimated iterations to convergence 275 setup time was (sec) 0.9300000 now iterating at: 14:11:01 rms-change max change #iterations 7.779605 384.5229 at 10iterations 4.359970 124.5674 at 20iterations 2.438021 58.09934 at 30iterations 1.357824 31.04823 at 40iterations 0.7545509 20.02182 at 50iterations 0.4208427 10.56305 at 60iterations 0.2337584 6.011078 at 70iterations 0.1302848 3.050098 at 80iterations 7.2355814E-02 1.645327 at 90iterations 4.0216438E-02 0.9573174 at 100iterations 2.2367202E-02 0.5236607 at 110iterations 1.2434750E-02 0.2757549 at 120iterations 6.9164960E-03 0.1541138 at 130iterations 3.8464204E-03 8.6393356E-02 at 140iterations 2.1368838E-03 4.6234131E-02 at 150iterations 1.1868520E-03 2.7386189E-02 at 160iterations 6.5919285E-04 1.3846397E-02 at 170iterations 3.6692142E-04 7.9689026E-03 at 180iterations finished qdiffx linear iterations at : 14:11:26 total time elapsed so far: 13.34000 # loops : 180 mean,max change (kT/e) : 3.6692142E-04 7.9689026E-03 energy calculations done at 13.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.47000 DelPhi exited at 14:11:27 13.469u 0.264s 0:27.14 50.5% 0+0k 0+0io 0pf+0w