Sun Oct 9 15:59:16 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 15:59:16 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 = 5657 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 0.4864385 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): 66.87800 138.0990 ymin,ymax (A): -11.99500 56.59600 zmin,zma (A): -3.191000 69.99400 x,y,z range (A): 71.22100 68.59100 73.18501 scale (grids/A): 0.4864385 object centre (A): 102.4885 22.30050 33.40150 number of atom coordinates read : 5657 total number of charged atoms : 5483 net assigned charge : -3.499963 assigned positive charge : 870.8080 centred at (gu) : 89.02435 90.66536 90.10370 assigned negative charge : -874.3160 centred at (gu) : 89.04619 90.62533 90.13008 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 8154 nv = 96 ne = 84 npr = 114726 no. pairs analyzed = 114726 no. exposed pairs = 6588 no. arc points = 45834 no. surface atoms = 2219 nbur = 3438 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= 248 mr = 4383 m= 0 mr = 1 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.5300000 number of dielectric boundary points 4018 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4353 ## 765 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 11128 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1272105E-11 -4.6309432E-11 midg,1,midg; midg,igrid,midg -4.9770032E-11 3.1656316E-11 1,midg,midg; igrid,midg,midg 9.1614173E-12 -3.0699377E-11 gauss-seidel spectral radius is 0.9784486 estimated iterations to convergence 56 setup time was (sec) 0.7500000 now iterating at: 15:59:17 rms-change max change #iterations 5.6517936E-02 9.229721 at 10iterations 5.1480634E-03 0.9359055 at 20iterations 1.5450689E-03 0.3019333 at 30iterations 5.3630705E-04 0.1060829 at 40iterations 1.8665956E-04 3.7025452E-02 at 50iterations finished qdiffx linear iterations at : 15:59:19 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.8665956E-04 3.7025452E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 15:59:20 3.350u 0.138s 0:03.83 90.8% 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 Sun Oct 9 2011 at 15:59:20 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 = 5657 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: 1.459315 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): 66.87800 138.0990 ymin,ymax (A): -11.99500 56.59600 zmin,zma (A): -3.191000 69.99400 x,y,z range (A): 71.22100 68.59100 73.18501 scale (grids/A): 1.459315 object centre (A): 102.4885 22.30050 33.40150 number of atom coordinates read : 5657 total number of charged atoms : 5483 net assigned charge : -3.499963 assigned positive charge : 870.8080 centred at (gu) : 87.07076 91.99422 90.30915 assigned negative charge : -874.3160 centred at (gu) : 87.13826 91.87595 90.39005 start vw surface at 0.2300000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 94303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45834 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 26123 mr = 66211 m= 1981 mr = 17703 m= 35 mr = 823 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 2799 time to turn everything in is 0.6500000 number of dielectric boundary points 37705 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 703 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 40373 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) : 0.4864385 object centre at (A) : 102.4885 22.30050 33.40150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4558005E-04 5.6797788E-03 midg,1,midg; midg,igrid,midg -5.3295391E-03 1.0554818E-02 1,midg,midg; igrid,midg,midg -2.5906814E-02 -1.6841105E-03 gauss-seidel spectral radius is 0.9979576 estimated iterations to convergence 176 setup time was (sec) 0.9300000 now iterating at: 15:59:21 rms-change max change #iterations 3.736425 155.8958 at 10iterations 1.482663 53.81087 at 20iterations 0.5875614 18.80870 at 30iterations 0.2326159 7.466461 at 40iterations 9.2805974E-02 2.827035 at 50iterations 3.6923662E-02 1.154826 at 60iterations 1.4962861E-02 0.4807234 at 70iterations 6.2106438E-03 0.2064056 at 80iterations 2.7989137E-03 0.1038361 at 90iterations 1.4146580E-03 5.7102203E-02 at 100iterations 8.1930746E-04 3.4187317E-02 at 110iterations 5.2031543E-04 2.0221710E-02 at 120iterations finished qdiffx linear iterations at : 15:59:27 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 5.2031543E-04 2.0221710E-02 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.170000 DelPhi exited at 15:59:27 7.173u 0.174s 0:07.74 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 Sun Oct 9 2011 at 15:59:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5657 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.2200000 grid size : 179 scale,in grids/A, set to be: 2.188973 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): 66.87800 138.0990 ymin,ymax (A): -11.99500 56.59600 zmin,zma (A): -3.191000 69.99400 x,y,z range (A): 71.22100 68.59100 73.18501 scale (grids/A): 2.188973 object centre (A): 102.4885 22.30050 33.40150 number of atom coordinates read : 5657 total number of charged atoms : 5483 net assigned charge : -3.499963 assigned positive charge : 870.8080 centred at (gu) : 85.60537 92.99102 90.46346 assigned negative charge : -874.3160 centred at (gu) : 85.70738 92.81390 90.58505 start vw surface at 0.2900000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 220936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45834 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 96179 mr = 163538 m= 22384 mr = 75867 m= 2600 mr = 16225 m= 90 mr = 1477 m= 0 mr = 15 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 9354 time to turn everything in is 1.590000 number of dielectric boundary points 85067 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 43650 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) : 1.459315 object centre at (A) : 102.4885 22.30050 33.40150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2085217E-02 0.2956126 midg,1,midg; midg,igrid,midg -0.1202884 0.2990837 1,midg,midg; igrid,midg,midg -0.7339470 6.9872133E-02 gauss-seidel spectral radius is 0.9991243 estimated iterations to convergence 267 setup time was (sec) 1.880000 now iterating at: 15:59:29 rms-change max change #iterations 10.43928 258.3175 at 10iterations 5.836694 179.2599 at 20iterations 3.262961 74.63239 at 30iterations 1.810795 37.12567 at 40iterations 1.002489 21.77561 at 50iterations 0.5528890 11.01914 at 60iterations 0.3043430 6.579872 at 70iterations 0.1672115 3.426460 at 80iterations 9.1895573E-02 1.784246 at 90iterations 5.0509378E-02 0.8982124 at 100iterations 2.7776210E-02 0.6066279 at 110iterations 1.5241080E-02 0.2715015 at 120iterations 8.4145144E-03 0.1559601 at 130iterations 4.6536005E-03 8.7083817E-02 at 140iterations 2.5886812E-03 4.8905134E-02 at 150iterations 1.4692573E-03 3.1101227E-02 at 160iterations 8.5455098E-04 1.8526077E-02 at 170iterations 5.1733555E-04 1.1310577E-02 at 180iterations finished qdiffx linear iterations at : 15:59:40 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 5.1733555E-04 1.1310577E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 15:59:41 12.819u 0.187s 0:13.30 97.6% 0+0k 0+0io 0pf+0w