Mon Oct 10 17:07:19 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 17:07:19 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 !!! WARNING: LEU 314 has a net charge of 0.5000 !!! WARNING: ADP 315 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6091823 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): -33.46400 23.57000 ymin,ymax (A): 38.37800 86.48100 zmin,zma (A): 0.1770000 58.61600 x,y,z range (A): 57.03400 48.10300 58.43900 scale (grids/A): 0.6091823 object centre (A): -4.947001 62.42950 29.39650 number of atom coordinates read : 2803 total number of charged atoms : 2663 net assigned charge : 2.000012 assigned positive charge : 425.8363 centred at (gu) : 91.73264 89.90552 89.21526 assigned negative charge : -423.8371 centred at (gu) : 91.68597 89.92316 89.26910 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6815 nv = 96 ne = 84 npr = 57335 no. pairs analyzed = 57335 no. exposed pairs = 3717 no. arc points = 25414 no. surface atoms = 1268 nbur = 1535 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3545 m= 0 mr = 40 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2650 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8643 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6388027E-09 -1.4750788E-09 midg,1,midg; midg,igrid,midg 2.0409512E-09 1.4284268E-10 1,midg,midg; igrid,midg,midg -9.2573882E-10 5.2034412E-09 gauss-seidel spectral radius is 0.9860685 estimated iterations to convergence 69 setup time was (sec) 0.6200000 now iterating at: 17:07:21 rms-change max change #iterations 0.1227061 18.68321 at 10iterations 1.0806791E-02 1.475353 at 20iterations 9.6492050E-04 0.1549187 at 30iterations 1.0709203E-04 1.8074036E-02 at 40iterations 2.4951294E-05 5.1813126E-03 at 50iterations finished qdiffx linear iterations at : 17:07:25 total time elapsed so far: 4.520000 # loops : 50 mean,max change (kT/e) : 2.4951294E-05 5.1813126E-03 energy calculations done at 4.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.700000 DelPhi exited at 17:07:27 4.704u 0.432s 0:07.18 71.4% 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 17:07:27 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 !!! WARNING: LEU 314 has a net charge of 0.5000 !!! WARNING: ADP 315 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.827547 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): -33.46400 23.57000 ymin,ymax (A): 38.37800 86.48100 zmin,zma (A): 0.1770000 58.61600 x,y,z range (A): 57.03400 48.10300 58.43900 scale (grids/A): 1.827547 object centre (A): -4.947001 62.42950 29.39650 number of atom coordinates read : 2803 total number of charged atoms : 2663 net assigned charge : 2.000012 assigned positive charge : 425.8363 centred at (gu) : 95.19730 89.71602 87.64514 assigned negative charge : -423.8371 centred at (gu) : 95.05760 89.76891 87.80687 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25414 grid for indexing accessible points = 1.400000 m= 24807 mr = 49959 m= 3420 mr = 17450 m= 160 mr = 1914 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 33093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 205 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20849 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) : 0.6091823 object centre at (A) : -4.947001 62.42950 29.39650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7583428E-02 -4.3572202E-02 midg,1,midg; midg,igrid,midg 5.9206444E-03 9.2892349E-03 1,midg,midg; igrid,midg,midg -1.1096487E-02 1.0177214E-02 gauss-seidel spectral radius is 0.9985427 estimated iterations to convergence 208 setup time was (sec) 0.9400000 now iterating at: 17:07:28 rms-change max change #iterations 4.150465 190.8168 at 10iterations 1.885493 61.66616 at 20iterations 0.8640596 27.82154 at 30iterations 0.3935833 15.80938 at 40iterations 0.1800660 5.930367 at 50iterations 8.2364865E-02 2.533455 at 60iterations 3.7641909E-02 1.183334 at 70iterations 1.7178545E-02 0.5407505 at 80iterations 7.8688134E-03 0.2514343 at 90iterations 3.5996777E-03 0.1118577 at 100iterations 1.6637942E-03 5.4069519E-02 at 110iterations 7.7998341E-04 2.6481628E-02 at 120iterations finished qdiffx linear iterations at : 17:07:42 total time elapsed so far: 11.12000 # loops : 120 mean,max change (kT/e) : 7.7998341E-04 2.6481628E-02 energy calculations done at 11.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.30000 DelPhi exited at 17:07:43 11.301u 0.497s 0:16.61 70.9% 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 Mon Oct 10 2011 at 17:07:43 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 !!! WARNING: LEU 314 has a net charge of 0.5000 !!! WARNING: ADP 315 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.741320 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): -33.46400 23.57000 ymin,ymax (A): 38.37800 86.48100 zmin,zma (A): 0.1770000 58.61600 x,y,z range (A): 57.03400 48.10300 58.43900 scale (grids/A): 2.741320 object centre (A): -4.947001 62.42950 29.39650 number of atom coordinates read : 2803 total number of charged atoms : 2663 net assigned charge : 2.000012 assigned positive charge : 425.8363 centred at (gu) : 97.79562 89.57391 86.46729 assigned negative charge : -423.8371 centred at (gu) : 97.58633 89.65324 86.71035 start vw surface at 0.1200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 171369 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25414 grid for indexing accessible points = 1.400000 m= 82215 mr = 121673 m= 27110 mr = 65400 m= 5751 mr = 20879 m= 687 mr = 4076 m= 33 mr = 385 m= 0 mr = 4 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.580000 number of dielectric boundary points 74748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 21301 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) : 1.827547 object centre at (A) : -4.947001 62.42950 29.39650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7393435 -0.8966382 midg,1,midg; midg,igrid,midg 1.8620003E-02 0.1407914 1,midg,midg; igrid,midg,midg -7.3853247E-02 0.1002664 gauss-seidel spectral radius is 0.9992424 estimated iterations to convergence 287 setup time was (sec) 1.930000 now iterating at: 17:07:46 rms-change max change #iterations 10.04924 394.9330 at 10iterations 5.888227 128.3158 at 20iterations 3.422045 79.41904 at 30iterations 1.985133 42.51797 at 40iterations 1.149318 27.04016 at 50iterations 0.6614198 13.34902 at 60iterations 0.3804787 8.356648 at 70iterations 0.2184619 4.440943 at 80iterations 0.1249959 2.597401 at 90iterations 7.1706258E-02 1.256142 at 100iterations 4.1001778E-02 0.7483239 at 110iterations 2.3501376E-02 0.4304490 at 120iterations 1.3480180E-02 0.2557487 at 130iterations 7.6942104E-03 0.1432066 at 140iterations 4.4183736E-03 7.9109192E-02 at 150iterations 2.5386023E-03 4.5610428E-02 at 160iterations 1.4655757E-03 2.6548386E-02 at 170iterations 8.5338735E-04 1.8329620E-02 at 180iterations finished qdiffx linear iterations at : 17:08:09 total time elapsed so far: 20.25000 # loops : 180 mean,max change (kT/e) : 8.5338735E-04 1.8329620E-02 energy calculations done at 20.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.43000 DelPhi exited at 17:08:10 20.434u 0.525s 0:26.45 79.2% 0+0k 0+0io 0pf+0w