Sat Oct 8 23:51:54 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 Sat Oct 8 2011 at 23:51:54 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 = 2402 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6521221 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): 1.9000053E-02 53.08800 ymin,ymax (A): 8.092000 49.75800 zmin,zma (A): -6.349000 48.24200 x,y,z range (A): 53.06900 41.66600 54.59100 scale (grids/A): 0.6521221 object centre (A): 26.55350 28.92500 20.94650 number of atom coordinates read : 2402 total number of charged atoms : 2267 net assigned charge : 12.50002 assigned positive charge : 350.5763 centred at (gu) : 90.08337 90.84869 88.99057 assigned negative charge : -338.0771 centred at (gu) : 90.09274 90.80437 88.98327 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6877 nv = 96 ne = 84 npr = 48882 no. pairs analyzed = 48882 no. exposed pairs = 3113 no. arc points = 22141 no. surface atoms = 1043 nbur = 1359 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 396 mr = 3659 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2800000 number of dielectric boundary points 3562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2225 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8222 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0093545E-08 2.1653371E-08 midg,1,midg; midg,igrid,midg 1.6297742E-08 3.7784954E-08 1,midg,midg; igrid,midg,midg 2.6391671E-08 2.4625072E-08 gauss-seidel spectral radius is 0.9878019 estimated iterations to convergence 74 setup time was (sec) 0.5300000 now iterating at: 23:51:55 rms-change max change #iterations 0.1477755 22.19825 at 10iterations 1.5688393E-02 2.387758 at 20iterations 1.6954619E-03 0.2786303 at 30iterations 2.9375532E-04 5.3947449E-02 at 40iterations 9.0540256E-05 1.7726898E-02 at 50iterations finished qdiffx linear iterations at : 23:51:58 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 9.0540256E-05 1.7726898E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 23:51:58 3.441u 0.241s 0:03.97 92.6% 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 Sat Oct 8 2011 at 23:51:58 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 = 2402 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: 1.956366 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): 1.9000053E-02 53.08800 ymin,ymax (A): 8.092000 49.75800 zmin,zma (A): -6.349000 48.24200 x,y,z range (A): 53.06900 41.66600 54.59100 scale (grids/A): 1.956366 object centre (A): 26.55350 28.92500 20.94650 number of atom coordinates read : 2402 total number of charged atoms : 2267 net assigned charge : 12.50002 assigned positive charge : 350.5763 centred at (gu) : 90.24974 92.54553 86.97121 assigned negative charge : -338.0771 centred at (gu) : 90.27833 92.41302 86.94976 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73657 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22141 grid for indexing accessible points = 1.400000 m= 26896 mr = 49722 m= 4708 mr = 19618 m= 323 mr = 2876 m= 3 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1979 time to turn everything in is 0.5400000 number of dielectric boundary points 33239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 151 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17922 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) : 0.6521221 object centre at (A) : 26.55350 28.92500 20.94650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0402923E-02 5.5142872E-02 midg,1,midg; midg,igrid,midg 4.3181633E-03 3.2852400E-02 1,midg,midg; igrid,midg,midg 5.5758532E-02 4.8829120E-02 gauss-seidel spectral radius is 0.9986916 estimated iterations to convergence 219 setup time was (sec) 0.8500000 now iterating at: 23:51:59 rms-change max change #iterations 4.153191 181.2727 at 10iterations 1.982808 72.15368 at 20iterations 0.9394013 31.99615 at 30iterations 0.4474405 14.34350 at 40iterations 0.2126419 7.802828 at 50iterations 0.1008403 3.302611 at 60iterations 4.7878150E-02 1.419508 at 70iterations 2.2945389E-02 0.7132931 at 80iterations 1.0934637E-02 0.3552150 at 90iterations 5.2518216E-03 0.1634083 at 100iterations 2.5593203E-03 8.0322266E-02 at 110iterations 1.2760123E-03 4.0720940E-02 at 120iterations finished qdiffx linear iterations at : 23:52:06 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.2760123E-03 4.0720940E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 23:52:07 7.787u 0.248s 0:08.32 96.3% 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 Sat Oct 8 2011 at 23:52:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 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: 2.934550 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): 1.9000053E-02 53.08800 ymin,ymax (A): 8.092000 49.75800 zmin,zma (A): -6.349000 48.24200 x,y,z range (A): 53.06900 41.66600 54.59100 scale (grids/A): 2.934550 object centre (A): 26.55350 28.92500 20.94650 number of atom coordinates read : 2402 total number of charged atoms : 2267 net assigned charge : 12.50002 assigned positive charge : 350.5763 centred at (gu) : 90.37462 93.81806 85.45681 assigned negative charge : -338.0771 centred at (gu) : 90.41740 93.61966 85.42466 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 169976 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22141 grid for indexing accessible points = 1.400000 m= 85642 mr = 120616 m= 32528 mr = 69350 m= 8685 mr = 25976 m= 1403 mr = 6505 m= 113 mr = 924 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 6782 time to turn everything in is 1.370000 number of dielectric boundary points 74925 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 18134 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) : 1.956366 object centre at (A) : 26.55350 28.92500 20.94650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4689127 0.7777532 midg,1,midg; midg,igrid,midg 1.8712288E-02 0.3076722 1,midg,midg; igrid,midg,midg 0.5655899 0.4585356 gauss-seidel spectral radius is 0.9992794 estimated iterations to convergence 294 setup time was (sec) 1.690000 now iterating at: 23:52:08 rms-change max change #iterations 9.862198 419.3247 at 10iterations 5.878376 161.2519 at 20iterations 3.473858 68.78035 at 30iterations 2.039442 45.43997 at 40iterations 1.198607 25.92505 at 50iterations 0.6993886 13.24048 at 60iterations 0.4093412 7.362131 at 70iterations 0.2384172 4.485084 at 80iterations 0.1386681 2.545880 at 90iterations 8.0563888E-02 1.495486 at 100iterations 4.6999015E-02 0.9667130 at 110iterations 2.7277011E-02 0.4815617 at 120iterations 1.5859159E-02 0.3170738 at 130iterations 9.2265308E-03 0.1742344 at 140iterations 5.3667002E-03 9.8211288E-02 at 150iterations 3.1399543E-03 5.6751251E-02 at 160iterations 1.8448324E-03 3.8087845E-02 at 170iterations 1.1032386E-03 2.3035049E-02 at 180iterations finished qdiffx linear iterations at : 23:52:20 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 1.1032386E-03 2.3035049E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.07000 DelPhi exited at 23:52:20 13.070u 0.266s 0:13.61 97.9% 0+0k 0+0io 0pf+0w