Tue Oct 11 07:51:40 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 Tue Oct 11 2011 at 07:51:40 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 = 2358 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: 0.6373417 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): -9.058001 39.75000 ymin,ymax (A): -14.93800 40.91900 zmin,zma (A): 5.456000 52.57900 x,y,z range (A): 48.80800 55.85700 47.12300 scale (grids/A): 0.6373417 object centre (A): 15.34600 12.99050 29.01750 number of atom coordinates read : 2358 total number of charged atoms : 2222 net assigned charge : 4.500007 assigned positive charge : 352.3773 centred at (gu) : 89.50353 88.81094 90.57713 assigned negative charge : -347.8778 centred at (gu) : 89.42519 88.82894 90.73777 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 6518 nv = 96 ne = 84 npr = 47030 no. pairs analyzed = 47030 no. exposed pairs = 2863 no. arc points = 20402 no. surface atoms = 973 nbur = 1385 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3631 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.4100000 number of dielectric boundary points 3166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1991 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 7719 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9000991E-08 -1.1028794E-08 midg,1,midg; midg,igrid,midg 1.0208992E-08 3.4961614E-09 1,midg,midg; igrid,midg,midg -1.6829841E-09 1.2351447E-08 gauss-seidel spectral radius is 0.9872256 estimated iterations to convergence 72 setup time was (sec) 0.7000000 now iterating at: 07:51:41 rms-change max change #iterations 0.1351433 19.03014 at 10iterations 1.3411650E-02 1.905062 at 20iterations 1.3688058E-03 0.1855888 at 30iterations 1.5323803E-04 2.3834229E-02 at 40iterations 2.0170712E-05 3.2196045E-03 at 50iterations finished qdiffx linear iterations at : 07:51:44 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 2.0170712E-05 3.2196045E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 07:51:45 4.238u 0.200s 0:05.19 85.3% 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 Tue Oct 11 2011 at 07:51:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 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: 1.912025 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): -9.058001 39.75000 ymin,ymax (A): -14.93800 40.91900 zmin,zma (A): 5.456000 52.57900 x,y,z range (A): 48.80800 55.85700 47.12300 scale (grids/A): 1.912025 object centre (A): 15.34600 12.99050 29.01750 number of atom coordinates read : 2358 total number of charged atoms : 2222 net assigned charge : 4.500007 assigned positive charge : 352.3773 centred at (gu) : 88.51019 86.43261 91.73101 assigned negative charge : -347.8778 centred at (gu) : 88.27546 86.48666 92.21329 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 70044 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20402 grid for indexing accessible points = 1.400000 m= 26140 mr = 49063 m= 3927 mr = 19524 m= 243 mr = 2484 m= 3 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 795 time to turn everything in is 0.6700000 number of dielectric boundary points 29187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 17431 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) : 0.6373417 object centre at (A) : 15.34600 12.99050 29.01750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7607841E-02 -1.9409267E-02 midg,1,midg; midg,igrid,midg 2.6572952E-02 2.0421118E-02 1,midg,midg; igrid,midg,midg -4.5130299E-03 6.1819013E-03 gauss-seidel spectral radius is 0.9986227 estimated iterations to convergence 214 setup time was (sec) 1.020000 now iterating at: 07:51:46 rms-change max change #iterations 4.006562 187.4509 at 10iterations 1.868734 67.75865 at 20iterations 0.8794124 29.78121 at 30iterations 0.4096680 14.45816 at 40iterations 0.1917817 6.167586 at 50iterations 8.9999564E-02 3.008074 at 60iterations 4.1938018E-02 1.452362 at 70iterations 1.9630693E-02 0.6097777 at 80iterations 9.1863545E-03 0.2998505 at 90iterations 4.3238932E-03 0.1392441 at 100iterations 2.0200887E-03 6.4582825E-02 at 110iterations 9.5021218E-04 3.2714844E-02 at 120iterations finished qdiffx linear iterations at : 07:51:55 total time elapsed so far: 9.150000 # loops : 120 mean,max change (kT/e) : 9.5021218E-04 3.2714844E-02 energy calculations done at 9.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.410000 DelPhi exited at 07:51:55 9.415u 0.237s 0:10.25 94.0% 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 Oct 11 2011 at 07:51:55 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 = 2358 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.868038 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): -9.058001 39.75000 ymin,ymax (A): -14.93800 40.91900 zmin,zma (A): 5.456000 52.57900 x,y,z range (A): 48.80800 55.85700 47.12300 scale (grids/A): 2.868038 object centre (A): 15.34600 12.99050 29.01750 number of atom coordinates read : 2358 total number of charged atoms : 2222 net assigned charge : 4.500007 assigned positive charge : 352.3773 centred at (gu) : 87.76519 84.64890 92.59657 assigned negative charge : -347.8778 centred at (gu) : 87.41309 84.73001 93.31989 start vw surface at 0.1900000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 161919 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20402 grid for indexing accessible points = 1.400000 m= 84351 mr = 118509 m= 30370 mr = 69833 m= 6997 mr = 24558 m= 1063 mr = 5348 m= 64 mr = 760 m= 0 mr = 27 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 2907 time to turn everything in is 1.680000 number of dielectric boundary points 65729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 17768 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) : 1.912025 object centre at (A) : 15.34600 12.99050 29.01750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4400148 -0.2981154 midg,1,midg; midg,igrid,midg 0.2262117 0.2105334 1,midg,midg; igrid,midg,midg -2.6420636E-02 5.1842825E-03 gauss-seidel spectral radius is 0.9992483 estimated iterations to convergence 288 setup time was (sec) 2.050000 now iterating at: 07:51:58 rms-change max change #iterations 9.396073 284.8189 at 10iterations 5.468947 132.5813 at 20iterations 3.170042 72.94521 at 30iterations 1.830957 38.63326 at 40iterations 1.054090 20.79334 at 50iterations 0.6058677 10.79824 at 60iterations 0.3482443 7.099382 at 70iterations 0.1993242 4.053884 at 80iterations 0.1143465 1.999069 at 90iterations 6.5406173E-02 1.224837 at 100iterations 3.7496857E-02 0.6632743 at 110iterations 2.1572424E-02 0.4514058 at 120iterations 1.2302436E-02 0.2442389 at 130iterations 7.0436695E-03 0.1321793 at 140iterations 4.0529827E-03 8.0907941E-02 at 150iterations 2.3321421E-03 5.0140381E-02 at 160iterations 1.3445524E-03 2.5317192E-02 at 170iterations 7.8148209E-04 1.4593124E-02 at 180iterations finished qdiffx linear iterations at : 07:52:11 total time elapsed so far: 14.87000 # loops : 180 mean,max change (kT/e) : 7.8148209E-04 1.4593124E-02 energy calculations done at 14.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.11000 DelPhi exited at 07:52:12 15.110u 0.262s 0:16.10 95.4% 0+0k 0+0io 0pf+0w