Sun Oct 9 01:59:06 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 01:59:06 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 = 2393 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6272354 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): -27.10000 26.40300 ymin,ymax (A): -27.46400 15.28600 zmin,zma (A): -50.66600 6.091000 x,y,z range (A): 53.50300 42.75000 56.75700 scale (grids/A): 0.6272354 object centre (A): -0.3485003 -6.089001 -22.28750 number of atom coordinates read : 2393 total number of charged atoms : 2259 net assigned charge : 12.50002 assigned positive charge : 348.9393 centred at (gu) : 90.30338 90.54783 91.86079 assigned negative charge : -336.4401 centred at (gu) : 90.35361 90.48402 91.87788 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6412 nv = 96 ne = 84 npr = 47851 no. pairs analyzed = 47851 no. exposed pairs = 3105 no. arc points = 22160 no. surface atoms = 1038 nbur = 1355 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 3369 m= 0 mr = 31 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 69 time to turn everything in is 0.1800000 number of dielectric boundary points 3377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2187 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7674 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.2747428E-09 1.6710105E-08 midg,1,midg; midg,igrid,midg 7.1076727E-09 1.9070418E-08 1,midg,midg; igrid,midg,midg 1.5010412E-08 9.4908836E-09 gauss-seidel spectral radius is 0.9868248 estimated iterations to convergence 71 setup time was (sec) 0.3800000 now iterating at: 01:59:06 rms-change max change #iterations 0.1234903 18.23145 at 10iterations 1.2061440E-02 2.064892 at 20iterations 1.2578937E-03 0.2058678 at 30iterations 2.3468057E-04 4.5967102E-02 at 40iterations 7.1671115E-05 1.5823364E-02 at 50iterations finished qdiffx linear iterations at : 01:59:09 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 7.1671115E-05 1.5823364E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 01:59:10 3.499u 0.192s 0:04.04 91.0% 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 Sun Oct 9 2011 at 01:59:10 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 = 2393 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.881706 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): -27.10000 26.40300 ymin,ymax (A): -27.46400 15.28600 zmin,zma (A): -50.66600 6.091000 x,y,z range (A): 53.50300 42.75000 56.75700 scale (grids/A): 1.881706 object centre (A): -0.3485003 -6.089001 -22.28750 number of atom coordinates read : 2393 total number of charged atoms : 2259 net assigned charge : 12.50002 assigned positive charge : 348.9393 centred at (gu) : 90.90995 91.64301 95.58195 assigned negative charge : -336.4401 centred at (gu) : 91.06084 91.45208 95.63374 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 69225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22160 grid for indexing accessible points = 1.400000 m= 24103 mr = 46537 m= 3852 mr = 17389 m= 232 mr = 2365 m= 2 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1889 time to turn everything in is 0.3400000 number of dielectric boundary points 31048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 17793 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) : 0.6272354 object centre at (A) : -0.3485003 -6.089001 -22.28750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0511437E-02 3.9285354E-02 midg,1,midg; midg,igrid,midg 1.2149889E-03 2.2329438E-02 1,midg,midg; igrid,midg,midg 4.2425655E-02 4.2592164E-02 gauss-seidel spectral radius is 0.9985904 estimated iterations to convergence 211 setup time was (sec) 0.5600000 now iterating at: 01:59:10 rms-change max change #iterations 3.822523 162.0362 at 10iterations 1.757009 61.55499 at 20iterations 0.8146185 28.50138 at 30iterations 0.3746556 12.10540 at 40iterations 0.1735191 5.540299 at 50iterations 8.0231234E-02 2.698377 at 60iterations 3.7114404E-02 1.217976 at 70iterations 1.7167931E-02 0.5252851 at 80iterations 8.0069667E-03 0.3130970 at 90iterations 3.7231464E-03 0.1475178 at 100iterations 1.7642106E-03 6.3154221E-02 at 110iterations 8.5573539E-04 3.3672333E-02 at 120iterations finished qdiffx linear iterations at : 01:59:18 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 8.5573539E-04 3.3672333E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 01:59:18 7.975u 0.224s 0:08.48 96.5% 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 01:59:18 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 = 2393 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.822559 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): -27.10000 26.40300 ymin,ymax (A): -27.46400 15.28600 zmin,zma (A): -50.66600 6.091000 x,y,z range (A): 53.50300 42.75000 56.75700 scale (grids/A): 2.822559 object centre (A): -0.3485003 -6.089001 -22.28750 number of atom coordinates read : 2393 total number of charged atoms : 2259 net assigned charge : 12.50002 assigned positive charge : 348.9393 centred at (gu) : 91.36492 92.46443 98.37275 assigned negative charge : -336.4401 centred at (gu) : 91.59134 92.17816 98.45062 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 160061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22160 grid for indexing accessible points = 1.400000 m= 78651 mr = 113402 m= 28011 mr = 63127 m= 6825 mr = 22290 m= 1037 mr = 5039 m= 55 mr = 711 m= 0 mr = 11 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 6336 time to turn everything in is 0.8900000 number of dielectric boundary points 70060 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 18070 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) : 1.881706 object centre at (A) : -0.3485003 -6.089001 -22.28750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5769658 0.4528048 midg,1,midg; midg,igrid,midg -1.6069269E-02 0.2278361 1,midg,midg; igrid,midg,midg 0.4549325 0.4198910 gauss-seidel spectral radius is 0.9992481 estimated iterations to convergence 288 setup time was (sec) 1.130000 now iterating at: 01:59:20 rms-change max change #iterations 9.176369 463.5393 at 10iterations 5.368554 134.1685 at 20iterations 3.109996 80.00469 at 30iterations 1.804119 39.43242 at 40iterations 1.039033 22.98192 at 50iterations 0.5991254 11.93104 at 60iterations 0.3457667 6.886917 at 70iterations 0.1982343 3.994420 at 80iterations 0.1140982 2.326669 at 90iterations 6.5377556E-02 1.290918 at 100iterations 3.7540883E-02 0.6977150 at 110iterations 2.1564772E-02 0.4078445 at 120iterations 1.2395260E-02 0.2421951 at 130iterations 7.1407664E-03 0.1349888 at 140iterations 4.1354853E-03 8.3957672E-02 at 150iterations 2.4263805E-03 5.6024551E-02 at 160iterations 1.4601351E-03 3.0676603E-02 at 170iterations 9.0616959E-04 2.2399902E-02 at 180iterations finished qdiffx linear iterations at : 01:59:32 total time elapsed so far: 13.31000 # loops : 180 mean,max change (kT/e) : 9.0616959E-04 2.2399902E-02 energy calculations done at 13.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.44000 DelPhi exited at 01:59:32 13.444u 0.217s 0:13.92 98.0% 0+0k 0+0io 0pf+0w