Sun Oct 9 08:29:44 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 Sun Oct 9 2011 at 08:29:44 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 = 5751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4834592 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): 17.10700 80.73200 ymin,ymax (A): 17.92800 84.43400 zmin,zma (A): -5.059000 68.57700 x,y,z range (A): 63.62500 66.50600 73.63600 scale (grids/A): 0.4834592 object centre (A): 48.91950 51.18100 31.75900 number of atom coordinates read : 5751 total number of charged atoms : 5583 net assigned charge : -7.499964 assigned positive charge : 861.9342 centred at (gu) : 90.62706 89.73878 91.45211 assigned negative charge : -869.4417 centred at (gu) : 90.60570 89.77818 91.50185 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8414 nv = 96 ne = 84 npr = 115879 no. pairs analyzed = 115879 no. exposed pairs = 7308 no. arc points = 50557 no. surface atoms = 2450 nbur = 3301 mkacc time = 0.2500000 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 = 1.764000 m= 263 mr = 4213 m= 0 mr = 3 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.5200000 number of dielectric boundary points 4461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4825 ## 838 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 11441 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0736754E-11 -1.1312200E-10 midg,1,midg; midg,igrid,midg 7.7826426E-12 -6.1144409E-11 1,midg,midg; igrid,midg,midg -4.1196102E-11 -1.0949561E-11 gauss-seidel spectral radius is 0.9782037 estimated iterations to convergence 56 setup time was (sec) 0.7400000 now iterating at: 08:29:45 rms-change max change #iterations 5.6258526E-02 9.432384 at 10iterations 2.8792983E-03 0.5683193 at 20iterations 2.6124783E-04 6.2538147E-02 at 30iterations 5.2919706E-05 1.3370514E-02 at 40iterations 1.3501050E-05 3.1204224E-03 at 50iterations finished qdiffx linear iterations at : 08:29:47 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.3501050E-05 3.1204224E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 08:29:47 3.321u 0.121s 0:03.71 92.7% 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 08:29:48 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 = 5751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.450377 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): 17.10700 80.73200 ymin,ymax (A): 17.92800 84.43400 zmin,zma (A): -5.059000 68.57700 x,y,z range (A): 63.62500 66.50600 73.63600 scale (grids/A): 1.450377 object centre (A): 48.91950 51.18100 31.75900 number of atom coordinates read : 5751 total number of charged atoms : 5583 net assigned charge : -7.499964 assigned positive charge : 861.9342 centred at (gu) : 91.87926 89.21416 94.35481 assigned negative charge : -869.4417 centred at (gu) : 91.81670 89.33437 94.50500 start vw surface at 0.2200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 95528 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50557 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 26259 mr = 64468 m= 2007 mr = 16731 m= 38 mr = 751 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2075 time to turn everything in is 0.6600000 number of dielectric boundary points 41882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 804 ## 18 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 41053 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) : 0.4834592 object centre at (A) : 48.91950 51.18100 31.75900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9827895E-03 -3.3989523E-02 midg,1,midg; midg,igrid,midg -1.4441987E-03 -1.0032265E-02 1,midg,midg; igrid,midg,midg -1.1167333E-03 -1.4164323E-03 gauss-seidel spectral radius is 0.9979654 estimated iterations to convergence 176 setup time was (sec) 0.9300000 now iterating at: 08:29:49 rms-change max change #iterations 3.732246 195.2697 at 10iterations 1.479390 50.52454 at 20iterations 0.5858098 18.70252 at 30iterations 0.2327870 7.785675 at 40iterations 9.2673421E-02 3.259476 at 50iterations 3.6832936E-02 1.232010 at 60iterations 1.4615518E-02 0.4876251 at 70iterations 5.8423909E-03 0.1997151 at 80iterations 2.3196298E-03 7.4155807E-02 at 90iterations 9.3012553E-04 2.9462814E-02 at 100iterations 3.7451505E-04 1.1592865E-02 at 110iterations 1.5227940E-04 5.2642822E-03 at 120iterations finished qdiffx linear iterations at : 08:29:55 total time elapsed so far: 7.110000 # loops : 120 mean,max change (kT/e) : 1.5227940E-04 5.2642822E-03 energy calculations done at 7.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.310000 DelPhi exited at 08:29:55 7.315u 0.170s 0:07.82 95.6% 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 Sun Oct 9 2011 at 08:29:55 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 = 5751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.175566 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): 17.10700 80.73200 ymin,ymax (A): 17.92800 84.43400 zmin,zma (A): -5.059000 68.57700 x,y,z range (A): 63.62500 66.50600 73.63600 scale (grids/A): 2.175566 object centre (A): 48.91950 51.18100 31.75900 number of atom coordinates read : 5751 total number of charged atoms : 5583 net assigned charge : -7.499964 assigned positive charge : 861.9342 centred at (gu) : 92.81844 88.82082 96.53173 assigned negative charge : -869.4417 centred at (gu) : 92.72493 89.00149 96.75723 start vw surface at 0.2200000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 222724 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50557 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 96441 mr = 159299 m= 22283 mr = 73295 m= 2507 mr = 15305 m= 88 mr = 1396 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 6947 time to turn everything in is 1.550000 number of dielectric boundary points 94741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 44434 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) : 1.450377 object centre at (A) : 48.91950 51.18100 31.75900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3080468E-02 -0.9647426 midg,1,midg; midg,igrid,midg 4.8118848E-03 -0.1757586 1,midg,midg; igrid,midg,midg 4.0609512E-02 -1.8367803E-02 gauss-seidel spectral radius is 0.9991506 estimated iterations to convergence 271 setup time was (sec) 1.840000 now iterating at: 08:29:57 rms-change max change #iterations 10.58591 281.2851 at 10iterations 6.106724 144.4115 at 20iterations 3.484165 79.25514 at 30iterations 1.978136 42.60234 at 40iterations 1.122557 24.21910 at 50iterations 0.6322269 12.24354 at 60iterations 0.3550733 7.711494 at 70iterations 0.1993715 4.156364 at 80iterations 0.1115949 2.152571 at 90iterations 6.2290322E-02 1.308805 at 100iterations 3.4824129E-02 0.6751080 at 110iterations 1.9433724E-02 0.3545227 at 120iterations 1.0830745E-02 0.2127409 at 130iterations 6.0278033E-03 0.1159801 at 140iterations 3.3597399E-03 6.4340591E-02 at 150iterations 1.8708025E-03 3.7693024E-02 at 160iterations 1.0441234E-03 1.9779205E-02 at 170iterations 5.8339606E-04 1.0747194E-02 at 180iterations finished qdiffx linear iterations at : 08:30:07 total time elapsed so far: 11.50000 # loops : 180 mean,max change (kT/e) : 5.8339606E-04 1.0747194E-02 energy calculations done at 11.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.68000 DelPhi exited at 08:30:08 11.679u 0.165s 0:12.11 97.6% 0+0k 0+0io 0pf+0w