Mon Oct 10 10:32:47 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 Mon Oct 10 2011 at 10:32:47 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2888 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5604446 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): -22.07800 41.44300 ymin,ymax (A): -13.05600 45.71400 zmin,zma (A): -2.235000 51.07600 x,y,z range (A): 63.52100 58.77000 53.31100 scale (grids/A): 0.5604446 object centre (A): 9.682498 16.32900 24.42050 number of atom coordinates read : 2888 total number of charged atoms : 2735 net assigned charge : 5.014024 assigned positive charge : 425.6288 centred at (gu) : 92.25088 91.41467 86.75864 assigned negative charge : -420.6152 centred at (gu) : 92.28339 91.52255 86.54346 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6120 nv = 96 ne = 84 npr = 55921 no. pairs analyzed = 55921 no. exposed pairs = 4333 no. arc points = 31398 no. surface atoms = 1431 nbur = 1457 mkacc time = 0.1300000 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= 278 mr = 2708 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3094 ## 366 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7822 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7759165E-09 1.2999161E-09 midg,1,midg; midg,igrid,midg 1.2436805E-09 -7.1325373E-10 1,midg,midg; igrid,midg,midg 5.7449689E-10 5.0545246E-10 gauss-seidel spectral radius is 0.9835861 estimated iterations to convergence 64 setup time was (sec) 0.5500000 now iterating at: 10:32:48 rms-change max change #iterations 8.0592282E-02 14.44180 at 10iterations 5.6970636E-03 1.140251 at 20iterations 4.1820755E-04 8.1447601E-02 at 30iterations 4.3180942E-05 6.4053535E-03 at 40iterations 8.2395782E-06 1.0271072E-03 at 50iterations finished qdiffx linear iterations at : 10:32:50 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 8.2395782E-06 1.0271072E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 10:32:51 3.321u 0.183s 0:03.79 92.3% 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 Mon Oct 10 2011 at 10:32:51 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2888 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.681334 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): -22.07800 41.44300 ymin,ymax (A): -13.05600 45.71400 zmin,zma (A): -2.235000 51.07600 x,y,z range (A): 63.52100 58.77000 53.31100 scale (grids/A): 1.681334 object centre (A): 9.682498 16.32900 24.42050 number of atom coordinates read : 2888 total number of charged atoms : 2735 net assigned charge : 5.014024 assigned positive charge : 425.6288 centred at (gu) : 96.75211 94.24332 80.27562 assigned negative charge : -420.6152 centred at (gu) : 96.84983 94.56735 79.63021 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 66099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31398 grid for indexing accessible points = 1.400000 m= 20148 mr = 40736 m= 2167 mr = 12624 m= 58 mr = 905 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 34207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 306 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 21115 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) : 0.5604446 object centre at (A) : 9.682498 16.32900 24.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4517120E-02 1.2624748E-02 midg,1,midg; midg,igrid,midg 2.2460364E-02 2.5867077E-03 1,midg,midg; igrid,midg,midg -1.5249375E-02 -6.4751660E-03 gauss-seidel spectral radius is 0.9982905 estimated iterations to convergence 192 setup time was (sec) 0.7800000 now iterating at: 10:32:52 rms-change max change #iterations 3.427449 149.7431 at 10iterations 1.455528 58.95681 at 20iterations 0.6176279 21.07460 at 30iterations 0.2640474 9.203451 at 40iterations 0.1121377 4.249464 at 50iterations 4.7778077E-02 1.650627 at 60iterations 2.0402757E-02 0.7541504 at 70iterations 8.6824466E-03 0.2994944 at 80iterations 3.7213450E-03 0.1372643 at 90iterations 1.5880867E-03 5.3276062E-02 at 100iterations 6.7929964E-04 2.4040222E-02 at 110iterations 2.9268043E-04 1.0547400E-02 at 120iterations finished qdiffx linear iterations at : 10:32:58 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 2.9268043E-04 1.0547400E-02 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.390000 DelPhi exited at 10:32:59 7.394u 0.229s 0:07.92 96.0% 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 Mon Oct 10 2011 at 10:32:59 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2888 !!! WARNING: HIT 235 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: 2.522001 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): -22.07800 41.44300 ymin,ymax (A): -13.05600 45.71400 zmin,zma (A): -2.235000 51.07600 x,y,z range (A): 63.52100 58.77000 53.31100 scale (grids/A): 2.522001 object centre (A): 9.682498 16.32900 24.42050 number of atom coordinates read : 2888 total number of charged atoms : 2735 net assigned charge : 5.014024 assigned positive charge : 425.6288 centred at (gu) : 100.1282 96.36484 75.41334 assigned negative charge : -420.6152 centred at (gu) : 100.2747 96.85079 74.44524 start vw surface at 0.1600000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 153059 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31398 grid for indexing accessible points = 1.400000 m= 68248 mr = 100876 m= 20153 mr = 50720 m= 3258 mr = 14100 m= 219 mr = 1879 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.160000 number of dielectric boundary points 77285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 21866 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) : 1.681334 object centre at (A) : 9.682498 16.32900 24.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1344611 0.1562124 midg,1,midg; midg,igrid,midg 0.4496278 3.2297742E-02 1,midg,midg; igrid,midg,midg -0.6297906 -0.1480932 gauss-seidel spectral radius is 0.9991775 estimated iterations to convergence 275 setup time was (sec) 1.490000 now iterating at: 10:33:01 rms-change max change #iterations 9.029905 283.9274 at 10iterations 5.220716 141.7996 at 20iterations 2.989352 82.67856 at 30iterations 1.704217 41.25558 at 40iterations 0.9649953 20.70149 at 50iterations 0.5440798 15.46267 at 60iterations 0.3065591 8.554037 at 70iterations 0.1719474 3.773492 at 80iterations 9.6040495E-02 2.263096 at 90iterations 5.3938791E-02 1.242849 at 100iterations 3.0109044E-02 0.7344050 at 110iterations 1.6817009E-02 0.3854108 at 120iterations 9.4142724E-03 0.2242851 at 130iterations 5.2428427E-03 0.1190577 at 140iterations 2.9279392E-03 6.5368652E-02 at 150iterations 1.6336923E-03 3.5167694E-02 at 160iterations 9.1043400E-04 1.8590927E-02 at 170iterations 5.0724263E-04 1.0515213E-02 at 180iterations finished qdiffx linear iterations at : 10:33:11 total time elapsed so far: 11.80000 # loops : 180 mean,max change (kT/e) : 5.0724263E-04 1.0515213E-02 energy calculations done at 11.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.98000 DelPhi exited at 10:33:11 11.981u 0.219s 0:12.48 97.6% 0+0k 0+0io 0pf+0w