Tue Oct 11 08:26:32 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 08:26:32 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3966 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: 0.5148600 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): -39.53900 29.60600 ymin,ymax (A): -20.79900 37.45900 zmin,zma (A): -53.58300 5.155000 x,y,z range (A): 69.14500 58.25800 58.73800 scale (grids/A): 0.5148600 object centre (A): -4.966501 8.330000 -24.21400 number of atom coordinates read : 3966 total number of charged atoms : 3768 net assigned charge : -6.499983 assigned positive charge : 600.3580 centred at (gu) : 88.83745 89.65408 90.38209 assigned negative charge : -606.8607 centred at (gu) : 88.74740 89.68398 90.27618 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6991 nv = 96 ne = 84 npr = 73856 no. pairs analyzed = 73856 no. exposed pairs = 5865 no. arc points = 42311 no. surface atoms = 1944 nbur = 2022 mkacc time = 0.1900000 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 = 1.652000 m= 260 mr = 3115 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 4136 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4067 ## 620 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9198 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5525735E-10 1.8431053E-10 midg,1,midg; midg,igrid,midg -3.3363191E-11 -1.7242388E-10 1,midg,midg; igrid,midg,midg -4.7529553E-10 9.1083564E-11 gauss-seidel spectral radius is 0.9806731 estimated iterations to convergence 59 setup time was (sec) 0.6700000 now iterating at: 08:26:33 rms-change max change #iterations 6.1660662E-02 10.73496 at 10iterations 3.5517542E-03 0.6472626 at 20iterations 2.7156016E-04 4.8481464E-02 at 30iterations 5.1645500E-05 7.5321198E-03 at 40iterations 1.3852670E-05 1.9733906E-03 at 50iterations finished qdiffx linear iterations at : 08:26:37 total time elapsed so far: 4.590000 # loops : 50 mean,max change (kT/e) : 1.3852670E-05 1.9733906E-03 energy calculations done at 4.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 08:26:37 4.775u 0.382s 0:05.54 92.9% 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 08:26:37 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3966 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: 1.544580 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): -39.53900 29.60600 ymin,ymax (A): -20.79900 37.45900 zmin,zma (A): -53.58300 5.155000 x,y,z range (A): 69.14500 58.25800 58.73800 scale (grids/A): 1.544580 object centre (A): -4.966501 8.330000 -24.21400 number of atom coordinates read : 3966 total number of charged atoms : 3768 net assigned charge : -6.499983 assigned positive charge : 600.3580 centred at (gu) : 86.51117 88.96141 91.14494 assigned negative charge : -606.8607 centred at (gu) : 86.24178 89.05137 90.82815 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 77510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42311 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20774 mr = 48248 m= 1622 mr = 12605 m= 33 mr = 486 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 448 time to turn everything in is 0.6500000 number of dielectric boundary points 38600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 567 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 28508 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) : 0.5148600 object centre at (A) : -4.966501 8.330000 -24.21400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0446320E-03 -9.5180568E-04 midg,1,midg; midg,igrid,midg -2.3488060E-03 -2.0546410E-03 1,midg,midg; igrid,midg,midg -5.1087081E-03 1.7914504E-02 gauss-seidel spectral radius is 0.9980995 estimated iterations to convergence 182 setup time was (sec) 1.000000 now iterating at: 08:26:39 rms-change max change #iterations 3.459081 150.8892 at 10iterations 1.403078 57.98522 at 20iterations 0.5698530 22.24668 at 30iterations 0.2319751 8.924374 at 40iterations 9.4543889E-02 3.378925 at 50iterations 3.8362734E-02 1.387495 at 60iterations 1.5662992E-02 0.5469778 at 70iterations 6.3950056E-03 0.2178650 at 80iterations 2.6129533E-03 9.1778278E-02 at 90iterations 1.0793100E-03 3.6986828E-02 at 100iterations 4.4485021E-04 1.6498566E-02 at 110iterations 1.8838262E-04 6.7965984E-03 at 120iterations finished qdiffx linear iterations at : 08:26:49 total time elapsed so far: 11.36000 # loops : 120 mean,max change (kT/e) : 1.8838262E-04 6.7965984E-03 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.53000 DelPhi exited at 08:26:49 11.534u 0.438s 0:12.25 97.6% 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 08:26:50 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3966 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: 2.316870 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): -39.53900 29.60600 ymin,ymax (A): -20.79900 37.45900 zmin,zma (A): -53.58300 5.155000 x,y,z range (A): 69.14500 58.25800 58.73800 scale (grids/A): 2.316870 object centre (A): -4.966501 8.330000 -24.21400 number of atom coordinates read : 3966 total number of charged atoms : 3768 net assigned charge : -6.499983 assigned positive charge : 600.3580 centred at (gu) : 84.76640 88.44177 91.71716 assigned negative charge : -606.8607 centred at (gu) : 84.36265 88.57710 91.24223 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 180316 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42311 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 74253 mr = 119939 m= 17866 mr = 54796 m= 2042 mr = 11775 m= 125 mr = 967 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 1494 time to turn everything in is 1.550000 number of dielectric boundary points 87103 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 30078 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) : 1.544580 object centre at (A) : -4.966501 8.330000 -24.21400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9557700E-02 -3.4673512E-02 midg,1,midg; midg,igrid,midg -2.3293549E-02 -3.9614484E-02 1,midg,midg; igrid,midg,midg 1.9281480E-03 0.4912097 gauss-seidel spectral radius is 0.9991472 estimated iterations to convergence 270 setup time was (sec) 1.940000 now iterating at: 08:26:52 rms-change max change #iterations 9.577229 334.9638 at 10iterations 5.506796 141.8895 at 20iterations 3.128276 82.09628 at 30iterations 1.770846 37.23650 at 40iterations 0.9958944 22.86860 at 50iterations 0.5577117 11.76079 at 60iterations 0.3112538 6.837524 at 70iterations 0.1733146 3.533529 at 80iterations 9.6188553E-02 1.879748 at 90iterations 5.3519096E-02 1.214691 at 100iterations 2.9631181E-02 0.5751975 at 110iterations 1.6391667E-02 0.3553455 at 120iterations 9.0622837E-03 0.1794949 at 130iterations 5.0138249E-03 9.5131874E-02 at 140iterations 2.7732234E-03 6.1063766E-02 at 150iterations 1.5321763E-03 3.1776428E-02 at 160iterations 8.4928150E-04 1.6654491E-02 at 170iterations 4.6886457E-04 8.8119507E-03 at 180iterations finished qdiffx linear iterations at : 08:27:10 total time elapsed so far: 19.70000 # loops : 180 mean,max change (kT/e) : 4.6886457E-04 8.8119507E-03 energy calculations done at 19.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.87000 DelPhi exited at 08:27:10 19.876u 0.443s 0:20.65 98.3% 0+0k 0+0io 0pf+0w