Sun Oct 9 07:14:00 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 07:14:00 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1750 !!! WARNING: NDP 163 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6753937 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): -24.98100 27.72900 ymin,ymax (A): 2.308000 47.85200 zmin,zma (A): -0.7350000 47.80400 x,y,z range (A): 52.71000 45.54400 48.53900 scale (grids/A): 0.6753937 object centre (A): 1.374000 25.08000 23.53450 number of atom coordinates read : 1750 total number of charged atoms : 1619 net assigned charge : -3.499994 assigned positive charge : 262.3424 centred at (gu) : 89.39685 91.37286 89.83598 assigned negative charge : -265.8423 centred at (gu) : 89.51536 91.24431 89.92773 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5373 nv = 96 ne = 84 npr = 37066 no. pairs analyzed = 37066 no. exposed pairs = 2110 no. arc points = 15289 no. surface atoms = 711 nbur = 1039 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 268 mr = 2959 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 124 time to turn everything in is 0.1500000 number of dielectric boundary points 2655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1431 ## 130 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6129 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3720756E-09 -3.1260281E-08 midg,1,midg; midg,igrid,midg -3.0146179E-08 1.5431866E-08 1,midg,midg; igrid,midg,midg 1.0776196E-08 -3.3402944E-08 gauss-seidel spectral radius is 0.9885561 estimated iterations to convergence 76 setup time was (sec) 0.3400000 now iterating at: 07:14:00 rms-change max change #iterations 0.1535079 28.64463 at 10iterations 1.7039295E-02 2.906073 at 20iterations 1.8834501E-03 0.3112812 at 30iterations 2.1235058E-04 3.7117004E-02 at 40iterations 2.3508584E-05 3.9672852E-03 at 50iterations finished qdiffx linear iterations at : 07:14:03 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 2.3508584E-05 3.9672852E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 07:14:03 3.329u 0.176s 0:03.78 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 Sun Oct 9 2011 at 07:14:03 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1750 !!! WARNING: NDP 163 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.026181 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): -24.98100 27.72900 ymin,ymax (A): 2.308000 47.85200 zmin,zma (A): -0.7350000 47.80400 x,y,z range (A): 52.71000 45.54400 48.53900 scale (grids/A): 2.026181 object centre (A): 1.374000 25.08000 23.53450 number of atom coordinates read : 1750 total number of charged atoms : 1619 net assigned charge : -3.499994 assigned positive charge : 262.3424 centred at (gu) : 88.19089 94.11901 89.50819 assigned negative charge : -265.8423 centred at (gu) : 88.54629 93.73325 89.78319 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 57228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15289 grid for indexing accessible points = 1.400000 m= 21035 mr = 39322 m= 3496 mr = 16035 m= 246 mr = 2315 m= 7 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 2607 time to turn everything in is 0.2900000 number of dielectric boundary points 24217 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 12819 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) : 0.6753937 object centre at (A) : 1.374000 25.08000 23.53450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6614481E-03 -3.2133806E-02 midg,1,midg; midg,igrid,midg -3.6936760E-02 3.7704866E-02 1,midg,midg; igrid,midg,midg -1.6362764E-02 -5.3769488E-02 gauss-seidel spectral radius is 0.9986979 estimated iterations to convergence 220 setup time was (sec) 0.5000000 now iterating at: 07:14:04 rms-change max change #iterations 3.936281 176.4125 at 10iterations 1.873178 87.60370 at 20iterations 0.8914469 35.74035 at 30iterations 0.4244462 16.02516 at 40iterations 0.2019512 7.002099 at 50iterations 9.6495599E-02 3.389974 at 60iterations 4.5730278E-02 1.677499 at 70iterations 2.1784503E-02 0.8026848 at 80iterations 1.0425572E-02 0.4351559 at 90iterations 4.9487478E-03 0.1650620 at 100iterations 2.3701647E-03 8.1691742E-02 at 110iterations 1.1266223E-03 3.8556814E-02 at 120iterations finished qdiffx linear iterations at : 07:14:11 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 1.1266223E-03 3.8556814E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 07:14:12 7.633u 0.201s 0:08.10 96.6% 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 07:14:12 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1750 !!! WARNING: NDP 163 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.039272 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): -24.98100 27.72900 ymin,ymax (A): 2.308000 47.85200 zmin,zma (A): -0.7350000 47.80400 x,y,z range (A): 52.71000 45.54400 48.53900 scale (grids/A): 3.039272 object centre (A): 1.374000 25.08000 23.53450 number of atom coordinates read : 1750 total number of charged atoms : 1619 net assigned charge : -3.499994 assigned positive charge : 262.3424 centred at (gu) : 87.28653 96.17851 89.26240 assigned negative charge : -265.8423 centred at (gu) : 87.81958 95.59980 89.67490 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 132239 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15289 grid for indexing accessible points = 1.400000 m= 66963 mr = 95041 m= 25429 mr = 55696 m= 6479 mr = 21078 m= 1054 mr = 5026 m= 95 mr = 739 m= 4 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 8759 time to turn everything in is 0.7500000 number of dielectric boundary points 54614 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 12952 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) : 2.026181 object centre at (A) : 1.374000 25.08000 23.53450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1574740E-02 -0.5661416 midg,1,midg; midg,igrid,midg -0.3989357 0.4791655 1,midg,midg; igrid,midg,midg -6.2322255E-02 -0.4495170 gauss-seidel spectral radius is 0.9992594 estimated iterations to convergence 290 setup time was (sec) 0.9700000 now iterating at: 07:14:13 rms-change max change #iterations 8.882912 435.2314 at 10iterations 5.104425 119.3582 at 20iterations 2.924087 83.75569 at 30iterations 1.676127 35.74939 at 40iterations 0.9579994 20.51534 at 50iterations 0.5499181 11.36131 at 60iterations 0.3153993 6.546407 at 70iterations 0.1805552 3.867561 at 80iterations 0.1033173 2.012346 at 90iterations 5.9198145E-02 1.191506 at 100iterations 3.3977374E-02 0.7211475 at 110iterations 1.9451397E-02 0.3982005 at 120iterations 1.1148186E-02 0.2221642 at 130iterations 6.3853706E-03 0.1204748 at 140iterations 3.6632787E-03 7.3856413E-02 at 150iterations 2.1049196E-03 4.1090012E-02 at 160iterations 1.2049403E-03 2.2871017E-02 at 170iterations 6.9182680E-04 1.4790535E-02 at 180iterations finished qdiffx linear iterations at : 07:14:24 total time elapsed so far: 11.89000 # loops : 180 mean,max change (kT/e) : 6.9182680E-04 1.4790535E-02 energy calculations done at 11.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 07:14:24 12.031u 0.202s 0:12.52 97.6% 0+0k 0+0io 0pf+0w