Sat Oct 8 15:58:15 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 15:58:15 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2321 !!! WARNING: ASL 705 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6479089 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): 24.76100 72.75400 ymin,ymax (A): -17.39800 29.30800 zmin,zma (A): -18.56500 36.38100 x,y,z range (A): 47.99300 46.70600 54.94600 scale (grids/A): 0.6479089 object centre (A): 48.75750 5.955000 8.907998 number of atom coordinates read : 2321 total number of charged atoms : 2230 net assigned charge : 3.900002 assigned positive charge : 343.8781 centred at (gu) : 90.56067 89.11919 90.22605 assigned negative charge : -339.9788 centred at (gu) : 90.62206 89.23110 90.26872 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6548 nv = 96 ne = 84 npr = 47538 no. pairs analyzed = 47538 no. exposed pairs = 2812 no. arc points = 19541 no. surface atoms = 964 nbur = 1357 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3656 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2800000 number of dielectric boundary points 3178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1888 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7857 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1829886E-08 1.6794117E-09 midg,1,midg; midg,igrid,midg 2.5341754E-08 -5.9611160E-09 1,midg,midg; igrid,midg,midg 1.3106678E-08 -9.2685704E-10 gauss-seidel spectral radius is 0.9876300 estimated iterations to convergence 73 setup time was (sec) 0.5500000 now iterating at: 15:58:16 rms-change max change #iterations 0.1464318 20.56537 at 10iterations 1.4773583E-02 2.434827 at 20iterations 1.5379447E-03 0.2335033 at 30iterations 1.6995543E-04 2.3704529E-02 at 40iterations 2.3347828E-05 3.9291382E-03 at 50iterations finished qdiffx linear iterations at : 15:58:19 total time elapsed so far: 4.450000 # loops : 50 mean,max change (kT/e) : 2.3347828E-05 3.9291382E-03 energy calculations done at 4.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 15:58:20 4.625u 0.384s 0:05.33 93.8% 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 15:58:20 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2321 !!! WARNING: ASL 705 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.943727 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): 24.76100 72.75400 ymin,ymax (A): -17.39800 29.30800 zmin,zma (A): -18.56500 36.38100 x,y,z range (A): 47.99300 46.70600 54.94600 scale (grids/A): 1.943727 object centre (A): 48.75750 5.955000 8.907998 number of atom coordinates read : 2321 total number of charged atoms : 2230 net assigned charge : 3.900002 assigned positive charge : 343.8781 centred at (gu) : 91.68123 87.35717 90.67791 assigned negative charge : -339.9788 centred at (gu) : 91.86607 87.69322 90.80618 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70565 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19541 grid for indexing accessible points = 1.400000 m= 25103 mr = 49511 m= 4148 mr = 18600 m= 249 mr = 2712 m= 6 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 902 time to turn everything in is 0.5800000 number of dielectric boundary points 29144 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 17603 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) : 0.6479089 object centre at (A) : 48.75750 5.955000 8.907998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1783508E-02 -1.7146224E-02 midg,1,midg; midg,igrid,midg 2.4374949E-02 -4.6942243E-03 1,midg,midg; igrid,midg,midg 9.1145709E-03 -4.2814460E-02 gauss-seidel spectral radius is 0.9986572 estimated iterations to convergence 216 setup time was (sec) 0.8800000 now iterating at: 15:58:21 rms-change max change #iterations 4.121531 175.9604 at 10iterations 1.939469 72.17886 at 20iterations 0.9171318 32.99521 at 30iterations 0.4327909 13.55653 at 40iterations 0.2042377 6.461384 at 50iterations 9.6092261E-02 3.036865 at 60iterations 4.5305397E-02 1.519336 at 70iterations 2.1427635E-02 0.7293603 at 80iterations 1.0078860E-02 0.3208289 at 90iterations 4.7703562E-03 0.1498141 at 100iterations 2.2428248E-03 7.1052760E-02 at 110iterations 1.0618398E-03 3.1569481E-02 at 120iterations finished qdiffx linear iterations at : 15:58:31 total time elapsed so far: 10.50000 # loops : 120 mean,max change (kT/e) : 1.0618398E-03 3.1569481E-02 energy calculations done at 10.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.68000 DelPhi exited at 15:58:31 10.681u 0.417s 0:11.38 97.4% 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 15:58:31 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2321 !!! WARNING: ASL 705 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.915590 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): 24.76100 72.75400 ymin,ymax (A): -17.39800 29.30800 zmin,zma (A): -18.56500 36.38100 x,y,z range (A): 47.99300 46.70600 54.94600 scale (grids/A): 2.915590 object centre (A): 48.75750 5.955000 8.907998 number of atom coordinates read : 2321 total number of charged atoms : 2230 net assigned charge : 3.900002 assigned positive charge : 343.8781 centred at (gu) : 92.52177 86.03571 91.01685 assigned negative charge : -339.9788 centred at (gu) : 92.79909 86.53983 91.20930 start vw surface at 0.1000000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 163340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19541 grid for indexing accessible points = 1.400000 m= 81155 mr = 119929 m= 29535 mr = 66548 m= 7775 mr = 23966 m= 1158 mr = 6041 m= 65 mr = 794 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 3039 time to turn everything in is 1.490000 number of dielectric boundary points 65722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 17839 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) : 1.943727 object centre at (A) : 48.75750 5.955000 8.907998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2008298 -0.2326852 midg,1,midg; midg,igrid,midg 0.1873752 -7.0386618E-02 1,midg,midg; igrid,midg,midg 9.5627017E-02 -0.5968179 gauss-seidel spectral radius is 0.9992592 estimated iterations to convergence 290 setup time was (sec) 1.820000 now iterating at: 15:58:34 rms-change max change #iterations 9.574310 480.2893 at 10iterations 5.572235 116.6212 at 20iterations 3.233718 68.93893 at 30iterations 1.872301 40.41498 at 40iterations 1.083190 22.23614 at 50iterations 0.6256538 11.43205 at 60iterations 0.3606459 6.654984 at 70iterations 0.2077520 4.076859 at 80iterations 0.1197107 2.330856 at 90iterations 6.8958677E-02 1.284525 at 100iterations 3.9658003E-02 0.7255673 at 110iterations 2.2778938E-02 0.4590187 at 120iterations 1.3126894E-02 0.2431984 at 130iterations 7.5414232E-03 0.1472759 at 140iterations 4.3422128E-03 8.2092285E-02 at 150iterations 2.4985466E-03 4.4746399E-02 at 160iterations 1.4416369E-03 2.6803970E-02 at 170iterations 8.3255582E-04 1.7768860E-02 at 180iterations finished qdiffx linear iterations at : 15:58:50 total time elapsed so far: 18.47000 # loops : 180 mean,max change (kT/e) : 8.3255582E-04 1.7768860E-02 energy calculations done at 18.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.64000 DelPhi exited at 15:58:51 18.640u 0.463s 0:19.37 98.6% 0+0k 0+0io 0pf+0w