Sat Oct 15 14:49:42 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 14:49:42 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2861 !!! WARNING: HIT 107 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5741751 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): 2.351000 64.35300 ymin,ymax (A): -24.57000 24.42100 zmin,zma (A): 2.049000 49.31700 x,y,z range (A): 62.00200 48.99100 47.26800 scale (grids/A): 0.5741751 object centre (A): 33.35200 -7.4500084E-02 25.68300 number of atom coordinates read : 2861 total number of charged atoms : 2720 net assigned charge : -1.985970 assigned positive charge : 432.6251 centred at (gu) : 89.31865 90.01824 90.29070 assigned negative charge : -434.6122 centred at (gu) : 89.35706 89.87288 90.45481 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6254 nv = 96 ne = 84 npr = 57069 no. pairs analyzed = 57069 no. exposed pairs = 3786 no. arc points = 26869 no. surface atoms = 1267 nbur = 1594 mkacc time = 0.1500000 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 = 1.512000 m= 304 mr = 3185 m= 4 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.3300000 number of dielectric boundary points 3361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2713 ## 294 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7969 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3352120E-09 -3.5495784E-09 midg,1,midg; midg,igrid,midg -2.9526206E-09 2.1947544E-09 1,midg,midg; igrid,midg,midg 3.9492135E-10 -8.7613478E-10 gauss-seidel spectral radius is 0.9843436 estimated iterations to convergence 66 setup time was (sec) 0.6700000 now iterating at: 14:49:43 rms-change max change #iterations 9.3436413E-02 15.03316 at 10iterations 7.1058529E-03 1.045505 at 20iterations 5.4973311E-04 8.3873749E-02 at 30iterations 4.2990076E-05 6.7920685E-03 at 40iterations 4.0586101E-06 8.3923340E-04 at 50iterations finished qdiffx linear iterations at : 14:49:48 total time elapsed so far: 5.240000 # loops : 50 mean,max change (kT/e) : 4.0586101E-06 8.3923340E-04 energy calculations done at 5.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.400000 DelPhi exited at 14:49:48 5.409u 0.444s 0:06.16 94.8% 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 15 2011 at 14:49:48 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2861 !!! WARNING: HIT 107 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.722525 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): 2.351000 64.35300 ymin,ymax (A): -24.57000 24.42100 zmin,zma (A): 2.049000 49.31700 x,y,z range (A): 62.00200 48.99100 47.26800 scale (grids/A): 1.722525 object centre (A): 33.35200 -7.4500084E-02 25.68300 number of atom coordinates read : 2861 total number of charged atoms : 2720 net assigned charge : -1.985970 assigned positive charge : 432.6251 centred at (gu) : 87.95509 90.05438 90.87135 assigned negative charge : -434.6122 centred at (gu) : 88.07075 89.61849 91.36405 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 68820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26869 grid for indexing accessible points = 1.400000 m= 21913 mr = 45862 m= 2670 mr = 15082 m= 104 mr = 1415 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1552 time to turn everything in is 0.6000000 number of dielectric boundary points 31121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 285 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 21116 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) : 0.5741751 object centre at (A) : 33.35200 -7.4500084E-02 25.68300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9347435E-03 -7.6345783E-03 midg,1,midg; midg,igrid,midg -2.2248251E-02 1.2095004E-02 1,midg,midg; igrid,midg,midg -1.2175479E-03 -3.9428394E-02 gauss-seidel spectral radius is 0.9983705 estimated iterations to convergence 197 setup time was (sec) 0.9600000 now iterating at: 14:49:50 rms-change max change #iterations 3.692374 160.2753 at 10iterations 1.599615 58.97186 at 20iterations 0.6977782 24.20566 at 30iterations 0.3037451 11.19195 at 40iterations 0.1327276 5.133355 at 50iterations 5.7634979E-02 2.143384 at 60iterations 2.5092572E-02 0.9367027 at 70iterations 1.0974054E-02 0.3985668 at 80iterations 4.8166742E-03 0.1747265 at 90iterations 2.0880182E-03 7.5139046E-02 at 100iterations 9.1260456E-04 3.3032596E-02 at 110iterations 3.9850213E-04 1.4137268E-02 at 120iterations finished qdiffx linear iterations at : 14:50:02 total time elapsed so far: 13.17000 # loops : 120 mean,max change (kT/e) : 3.9850213E-04 1.4137268E-02 energy calculations done at 13.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.34000 DelPhi exited at 14:50:03 13.348u 0.497s 0:14.21 97.3% 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 15 2011 at 14:50:03 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2861 !!! WARNING: HIT 107 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.583788 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): 2.351000 64.35300 ymin,ymax (A): -24.57000 24.42100 zmin,zma (A): 2.049000 49.31700 x,y,z range (A): 62.00200 48.99100 47.26800 scale (grids/A): 2.583788 object centre (A): 33.35200 -7.4500084E-02 25.68300 number of atom coordinates read : 2861 total number of charged atoms : 2720 net assigned charge : -1.985970 assigned positive charge : 432.6251 centred at (gu) : 86.93243 90.08104 91.30677 assigned negative charge : -434.6122 centred at (gu) : 87.10609 89.42765 92.04595 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 159892 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26869 grid for indexing accessible points = 1.400000 m= 74092 mr = 112426 m= 22915 mr = 58445 m= 4331 mr = 17323 m= 460 mr = 2978 m= 19 mr = 276 m= 0 mr = 13 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 4946 time to turn everything in is 1.490000 number of dielectric boundary points 70248 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 21750 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) : 1.722525 object centre at (A) : 33.35200 -7.4500084E-02 25.68300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7680057E-02 -8.7008759E-02 midg,1,midg; midg,igrid,midg -0.2585836 0.1850550 1,midg,midg; igrid,midg,midg 5.3942844E-02 -0.7542894 gauss-seidel spectral radius is 0.9991981 estimated iterations to convergence 279 setup time was (sec) 1.880000 now iterating at: 14:50:05 rms-change max change #iterations 9.312778 278.2325 at 10iterations 5.345374 142.6196 at 20iterations 3.036576 74.22806 at 30iterations 1.724031 43.29041 at 40iterations 0.9768340 20.29784 at 50iterations 0.5520688 12.16786 at 60iterations 0.3109815 6.444552 at 70iterations 0.1753802 3.699535 at 80iterations 9.8727889E-02 2.013954 at 90iterations 5.5481475E-02 1.217560 at 100iterations 3.1182453E-02 0.6819000 at 110iterations 1.7524524E-02 0.3919907 at 120iterations 9.8651061E-03 0.1850338 at 130iterations 5.5437591E-03 0.1106367 at 140iterations 3.1133895E-03 5.8629036E-02 at 150iterations 1.7542444E-03 3.4972191E-02 at 160iterations 9.9369674E-04 2.1058559E-02 at 170iterations 5.6295475E-04 1.2664795E-02 at 180iterations finished qdiffx linear iterations at : 14:50:24 total time elapsed so far: 21.06000 # loops : 180 mean,max change (kT/e) : 5.6295475E-04 1.2664795E-02 energy calculations done at 21.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.23000 DelPhi exited at 14:50:25 21.230u 0.514s 0:22.03 98.6% 0+0k 0+0io 0pf+0w