Sun Oct 9 13:37:07 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 Sun Oct 9 2011 at 13:37:07 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 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: 0.7087398 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): -0.4970000 45.46000 ymin,ymax (A): 36.37400 86.60400 zmin,zma (A): -22.33500 24.71500 x,y,z range (A): 45.95700 50.23000 47.05000 scale (grids/A): 0.7087398 object centre (A): 22.48150 61.48900 1.190001 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500019 assigned positive charge : 360.6473 centred at (gu) : 89.83015 89.82596 91.03448 assigned negative charge : -359.1476 centred at (gu) : 89.93102 90.04945 90.96101 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7987 nv = 96 ne = 84 npr = 48324 no. pairs analyzed = 48324 no. exposed pairs = 2956 no. arc points = 20370 no. surface atoms = 998 nbur = 1361 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 491 mr = 4475 m= 5 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3921 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1923 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8976 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5089959E-08 6.7613129E-08 midg,1,midg; midg,igrid,midg 1.4532881E-07 -1.1729470E-07 1,midg,midg; igrid,midg,midg 7.3282422E-08 -4.5688825E-08 gauss-seidel spectral radius is 0.9896508 estimated iterations to convergence 80 setup time was (sec) 0.5000000 now iterating at: 13:37:08 rms-change max change #iterations 0.2189758 31.75369 at 10iterations 2.7716519E-02 4.565613 at 20iterations 3.8180137E-03 0.5069302 at 30iterations 7.3613744E-04 0.1045914 at 40iterations 2.0866880E-04 3.3115387E-02 at 50iterations finished qdiffx linear iterations at : 13:37:10 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 2.0866880E-04 3.3115387E-02 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 13:37:11 3.060u 0.140s 0:03.51 91.1% 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 Sun Oct 9 2011 at 13:37:11 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.126220 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): -0.4970000 45.46000 ymin,ymax (A): 36.37400 86.60400 zmin,zma (A): -22.33500 24.71500 x,y,z range (A): 45.95700 50.23000 47.05000 scale (grids/A): 2.126220 object centre (A): 22.48150 61.48900 1.190001 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500019 assigned positive charge : 360.6473 centred at (gu) : 89.49021 89.47755 93.10320 assigned negative charge : -359.1476 centred at (gu) : 89.79277 90.14811 92.88269 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 84790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20370 grid for indexing accessible points = 1.400000 m= 32787 mr = 59414 m= 6036 mr = 24439 m= 587 mr = 3882 m= 17 mr = 298 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 36184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 17589 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) : 0.7087398 object centre at (A) : 22.48150 61.48900 1.190001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1212157E-03 2.1425197E-02 midg,1,midg; midg,igrid,midg 0.1002835 -7.6088235E-02 1,midg,midg; igrid,midg,midg 6.1076572E-03 -9.2494003E-03 gauss-seidel spectral radius is 0.9988680 estimated iterations to convergence 235 setup time was (sec) 0.9000000 now iterating at: 13:37:12 rms-change max change #iterations 5.029675 211.9687 at 10iterations 2.514102 87.84549 at 20iterations 1.253565 37.02190 at 30iterations 0.6299635 18.38808 at 40iterations 0.3157948 10.18819 at 50iterations 0.1587032 4.373596 at 60iterations 7.9778388E-02 2.450598 at 70iterations 3.9957654E-02 1.086666 at 80iterations 2.0169996E-02 0.5662994 at 90iterations 1.0247163E-02 0.3066616 at 100iterations 5.2442038E-03 0.1677017 at 110iterations 2.7411003E-03 8.1381798E-02 at 120iterations finished qdiffx linear iterations at : 13:37:18 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 2.7411003E-03 8.1381798E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 13:37:18 7.083u 0.185s 0:07.55 96.1% 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 Sun Oct 9 2011 at 13:37:18 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 3.189329 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): -0.4970000 45.46000 ymin,ymax (A): 36.37400 86.60400 zmin,zma (A): -22.33500 24.71500 x,y,z range (A): 45.95700 50.23000 47.05000 scale (grids/A): 3.189329 object centre (A): 22.48150 61.48900 1.190001 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500019 assigned positive charge : 360.6473 centred at (gu) : 89.23528 89.21607 94.65472 assigned negative charge : -359.1476 centred at (gu) : 89.68913 90.22206 94.32391 start vw surface at 0.2000000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 195478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20370 grid for indexing accessible points = 1.400000 m= 103309 mr = 143378 m= 40614 mr = 84984 m= 11414 mr = 32981 m= 2289 mr = 8616 m= 262 mr = 1714 m= 17 mr = 143 m= 0 mr = 6 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.920000 number of dielectric boundary points 81561 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 17736 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) : 2.126220 object centre at (A) : 22.48150 61.48900 1.190001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0121985E-02 0.3543366 midg,1,midg; midg,igrid,midg 1.661089 -0.8292724 1,midg,midg; igrid,midg,midg 1.7905353E-02 -4.3445967E-02 gauss-seidel spectral radius is 0.9993091 estimated iterations to convergence 300 setup time was (sec) 2.210000 now iterating at: 13:37:21 rms-change max change #iterations 11.26543 375.1421 at 10iterations 6.736270 134.3321 at 20iterations 4.017277 80.09435 at 30iterations 2.392001 47.57729 at 40iterations 1.417650 31.14540 at 50iterations 0.8386781 14.62384 at 60iterations 0.4945716 8.572012 at 70iterations 0.2924569 5.783166 at 80iterations 0.1724291 2.842039 at 90iterations 0.1017337 1.707260 at 100iterations 5.9836958E-02 1.024666 at 110iterations 3.5395633E-02 0.6236773 at 120iterations 2.1032119E-02 0.3881791 at 130iterations 1.2650935E-02 0.2173042 at 140iterations 7.7480813E-03 0.1597061 at 150iterations 4.8980401E-03 9.2033386E-02 at 160iterations 3.2546862E-03 7.1773529E-02 at 170iterations 2.2949802E-03 4.9194336E-02 at 180iterations finished qdiffx linear iterations at : 13:37:30 total time elapsed so far: 11.89000 # loops : 180 mean,max change (kT/e) : 2.2949802E-03 4.9194336E-02 energy calculations done at 11.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.06000 DelPhi exited at 13:37:31 12.061u 0.183s 0:12.51 97.8% 0+0k 0+0io 0pf+0w