Sat Oct 15 12:16:20 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 15 2011 at 12:16:20 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3190 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.5485023 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): -20.03600 32.78900 ymin,ymax (A): 53.99800 118.9020 zmin,zma (A): 0.2210000 53.00600 x,y,z range (A): 52.82500 64.90401 52.78500 scale (grids/A): 0.5485023 object centre (A): 6.376499 86.45000 26.61350 number of atom coordinates read : 3190 total number of charged atoms : 3045 net assigned charge : 7.014040 assigned positive charge : 473.5498 centred at (gu) : 90.27193 88.59933 90.64981 assigned negative charge : -466.5373 centred at (gu) : 90.28628 88.53852 90.56405 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6418 nv = 96 ne = 84 npr = 62995 no. pairs analyzed = 62995 no. exposed pairs = 4202 no. arc points = 29346 no. surface atoms = 1413 nbur = 1777 mkacc time = 0.1100000 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 = 1.540000 m= 262 mr = 3281 m= 0 mr = 4 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2975 ## 354 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8295 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4862972E-10 1.3291259E-09 midg,1,midg; midg,igrid,midg 1.0815216E-11 6.7269773E-10 1,midg,midg; igrid,midg,midg 5.5568261E-10 3.9889900E-10 gauss-seidel spectral radius is 0.9828833 estimated iterations to convergence 63 setup time was (sec) 0.4400000 now iterating at: 12:16:20 rms-change max change #iterations 7.9607196E-02 12.87983 at 10iterations 5.2309874E-03 0.9330292 at 20iterations 3.6066235E-04 6.5292358E-02 at 30iterations 2.8545544E-05 4.0826797E-03 at 40iterations 3.9817219E-06 6.4682961E-04 at 50iterations finished qdiffx linear iterations at : 12:16:24 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 3.9817219E-06 6.4682961E-04 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 12:16:24 3.686u 0.199s 0:04.20 92.1% 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 Sat Oct 15 2011 at 12:16:24 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3190 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.645507 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): -20.03600 32.78900 ymin,ymax (A): 53.99800 118.9020 zmin,zma (A): 0.2210000 53.00600 x,y,z range (A): 52.82500 64.90401 52.78500 scale (grids/A): 1.645507 object centre (A): 6.376499 86.45000 26.61350 number of atom coordinates read : 3190 total number of charged atoms : 3045 net assigned charge : 7.014040 assigned positive charge : 473.5498 centred at (gu) : 90.81477 85.79712 91.94853 assigned negative charge : -466.5373 centred at (gu) : 90.85876 85.61515 91.69175 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 70840 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29346 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 22308 mr = 47975 m= 2409 mr = 15019 m= 62 mr = 1063 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 282 time to turn everything in is 0.3700000 number of dielectric boundary points 31562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 312 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 23403 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) : 0.5485023 object centre at (A) : 6.376499 86.45000 26.61350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2799780E-03 3.1962262E-03 midg,1,midg; midg,igrid,midg 1.0229453E-02 1.7384086E-02 1,midg,midg; igrid,midg,midg 2.3205409E-02 7.0464693E-04 gauss-seidel spectral radius is 0.9982430 estimated iterations to convergence 189 setup time was (sec) 0.6100000 now iterating at: 12:16:25 rms-change max change #iterations 3.487303 154.4787 at 10iterations 1.472301 59.82338 at 20iterations 0.6217765 21.93150 at 30iterations 0.2625032 8.827106 at 40iterations 0.1104055 3.890556 at 50iterations 4.6658542E-02 1.489304 at 60iterations 1.9734366E-02 0.6562999 at 70iterations 8.3585139E-03 0.2945795 at 80iterations 3.5491325E-03 0.1281433 at 90iterations 1.4985943E-03 5.3221703E-02 at 100iterations 6.3447468E-04 2.1905899E-02 at 110iterations 2.7057136E-04 9.3421936E-03 at 120iterations finished qdiffx linear iterations at : 12:16:33 total time elapsed so far: 8.450000 # loops : 120 mean,max change (kT/e) : 2.7057136E-04 9.3421936E-03 energy calculations done at 8.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.580000 DelPhi exited at 12:16:33 8.583u 0.242s 0:09.19 95.9% 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 Sat Oct 15 2011 at 12:16:33 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3190 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.468261 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): -20.03600 32.78900 ymin,ymax (A): 53.99800 118.9020 zmin,zma (A): 0.2210000 53.00600 x,y,z range (A): 52.82500 64.90401 52.78500 scale (grids/A): 2.468261 object centre (A): 6.376499 86.45000 26.61350 number of atom coordinates read : 3190 total number of charged atoms : 3045 net assigned charge : 7.014040 assigned positive charge : 473.5498 centred at (gu) : 91.22202 83.69553 92.92258 assigned negative charge : -466.5373 centred at (gu) : 91.28800 83.42257 92.53764 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 164603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29346 grid for indexing accessible points = 1.400000 m= 76637 mr = 117695 m= 22353 mr = 59720 m= 3597 mr = 16405 m= 225 mr = 2186 m= 6 mr = 80 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 1030 time to turn everything in is 0.9000000 number of dielectric boundary points 71336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 24333 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) : 1.645507 object centre at (A) : 6.376499 86.45000 26.61350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1149939 3.3430308E-02 midg,1,midg; midg,igrid,midg 0.1613728 0.3693503 1,midg,midg; igrid,midg,midg 0.4584285 -1.9495815E-02 gauss-seidel spectral radius is 0.9991632 estimated iterations to convergence 273 setup time was (sec) 1.170000 now iterating at: 12:16:35 rms-change max change #iterations 9.049753 348.3480 at 10iterations 5.162259 148.8027 at 20iterations 2.909034 76.87367 at 30iterations 1.638404 42.29971 at 40iterations 0.9163004 19.69525 at 50iterations 0.5128604 10.44888 at 60iterations 0.2856867 6.236928 at 70iterations 0.1598638 3.312294 at 80iterations 8.8642746E-02 1.923466 at 90iterations 4.9320538E-02 1.014641 at 100iterations 2.7437314E-02 0.5688648 at 110iterations 1.5244856E-02 0.3267803 at 120iterations 8.4477384E-03 0.1809387 at 130iterations 4.6910509E-03 9.3873978E-02 at 140iterations 2.5998503E-03 5.1360607E-02 at 150iterations 1.4435926E-03 2.9962480E-02 at 160iterations 8.0183818E-04 1.6391754E-02 at 170iterations 4.4545523E-04 9.2997551E-03 at 180iterations finished qdiffx linear iterations at : 12:16:47 total time elapsed so far: 13.46000 # loops : 180 mean,max change (kT/e) : 4.4545523E-04 9.2997551E-03 energy calculations done at 13.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.59000 DelPhi exited at 12:16:48 13.593u 0.247s 0:14.22 97.2% 0+0k 0+0io 0pf+0w