Sat Oct 8 16:25:05 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 Sat Oct 8 2011 at 16:25:05 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 = 2292 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: 0.6317096 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): -2.010000 47.87800 ymin,ymax (A): -16.88800 29.40100 zmin,zma (A): -17.97900 38.37600 x,y,z range (A): 49.88800 46.28900 56.35500 scale (grids/A): 0.6317096 object centre (A): 22.93400 6.256499 10.19850 number of atom coordinates read : 2292 total number of charged atoms : 2233 net assigned charge : 4.000001 assigned positive charge : 341.8532 centred at (gu) : 89.96635 89.01483 89.34542 assigned negative charge : -337.8538 centred at (gu) : 90.00655 89.13194 89.39167 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6119 nv = 96 ne = 84 npr = 45993 no. pairs analyzed = 45993 no. exposed pairs = 2954 no. arc points = 20222 no. surface atoms = 1012 nbur = 1280 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 304 mr = 3296 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3086 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2039 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7586 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3925587E-09 6.2965222E-10 midg,1,midg; midg,igrid,midg 1.7080680E-08 -4.0904231E-09 1,midg,midg; igrid,midg,midg 7.7300140E-09 1.1783710E-09 gauss-seidel spectral radius is 0.9869929 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 16:25:05 rms-change max change #iterations 0.1220004 20.34739 at 10iterations 1.1998720E-02 1.737009 at 20iterations 1.2011019E-03 0.1738014 at 30iterations 1.5861272E-04 2.5198221E-02 at 40iterations 3.4860488E-05 6.4892769E-03 at 50iterations finished qdiffx linear iterations at : 16:25:09 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 3.4860488E-05 6.4892769E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 16:25:09 4.283u 0.231s 0:04.79 94.1% 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 Sat Oct 8 2011 at 16:25:10 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 = 2292 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: 1.895129 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): -2.010000 47.87800 ymin,ymax (A): -16.88800 29.40100 zmin,zma (A): -17.97900 38.37600 x,y,z range (A): 49.88800 46.28900 56.35500 scale (grids/A): 1.895129 object centre (A): 22.93400 6.256499 10.19850 number of atom coordinates read : 2292 total number of charged atoms : 2233 net assigned charge : 4.000001 assigned positive charge : 341.8532 centred at (gu) : 89.89850 87.04420 88.03571 assigned negative charge : -337.8538 centred at (gu) : 90.01952 87.39562 88.17483 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 66385 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20222 grid for indexing accessible points = 1.400000 m= 23560 mr = 45950 m= 3786 mr = 17108 m= 235 mr = 2385 m= 2 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 743 time to turn everything in is 0.6200000 number of dielectric boundary points 28450 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 17551 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) : 0.6317096 object centre at (A) : 22.93400 6.256499 10.19850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5279766E-02 -7.9553332E-03 midg,1,midg; midg,igrid,midg 1.6266437E-02 -4.1252975E-03 1,midg,midg; igrid,midg,midg 8.5630370E-03 -2.6176037E-02 gauss-seidel spectral radius is 0.9985911 estimated iterations to convergence 211 setup time was (sec) 0.9600000 now iterating at: 16:25:11 rms-change max change #iterations 3.916484 184.5410 at 10iterations 1.806149 72.40909 at 20iterations 0.8408853 30.84679 at 30iterations 0.3884397 13.71159 at 40iterations 0.1808782 5.989553 at 50iterations 8.3668731E-02 2.781240 at 60iterations 3.8726415E-02 1.226576 at 70iterations 1.7969297E-02 0.6260362 at 80iterations 8.3381664E-03 0.2961681 at 90iterations 3.8697410E-03 0.1420460 at 100iterations 1.7984139E-03 6.1988831E-02 at 110iterations 8.3978049E-04 2.7671814E-02 at 120iterations finished qdiffx linear iterations at : 16:25:19 total time elapsed so far: 9.640000 # loops : 120 mean,max change (kT/e) : 8.3978049E-04 2.7671814E-02 energy calculations done at 9.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.810000 DelPhi exited at 16:25:20 9.816u 0.298s 0:10.40 97.1% 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 Sat Oct 8 2011 at 16:25:20 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 = 2292 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: 2.842694 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): -2.010000 47.87800 ymin,ymax (A): -16.88800 29.40100 zmin,zma (A): -17.97900 38.37600 x,y,z range (A): 49.88800 46.28900 56.35500 scale (grids/A): 2.842694 object centre (A): 22.93400 6.256499 10.19850 number of atom coordinates read : 2292 total number of charged atoms : 2233 net assigned charge : 4.000001 assigned positive charge : 341.8532 centred at (gu) : 89.84769 85.56631 87.05350 assigned negative charge : -337.8538 centred at (gu) : 90.02924 86.09345 87.26221 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 153889 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20222 grid for indexing accessible points = 1.400000 m= 76359 mr = 111955 m= 27730 mr = 61857 m= 6845 mr = 22106 m= 1009 mr = 5139 m= 75 mr = 680 m= 3 mr = 33 m= 0 mr = 2 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 2258 time to turn everything in is 1.380000 number of dielectric boundary points 64138 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 17864 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) : 1.895129 object centre at (A) : 22.93400 6.256499 10.19850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3778540 -0.1601152 midg,1,midg; midg,igrid,midg 0.1316887 -6.1046451E-02 1,midg,midg; igrid,midg,midg 9.7529218E-02 -0.3674691 gauss-seidel spectral radius is 0.9992443 estimated iterations to convergence 287 setup time was (sec) 1.720000 now iterating at: 16:25:22 rms-change max change #iterations 9.276188 332.2922 at 10iterations 5.447755 128.8969 at 20iterations 3.171596 71.98498 at 30iterations 1.843903 44.34327 at 40iterations 1.065734 20.31502 at 50iterations 0.6149071 12.48686 at 60iterations 0.3539749 7.233788 at 70iterations 0.2033605 4.092859 at 80iterations 0.1167264 2.199219 at 90iterations 6.7140855E-02 1.230156 at 100iterations 3.8406804E-02 0.7624779 at 110iterations 2.2017231E-02 0.4251866 at 120iterations 1.2626139E-02 0.2501181 at 130iterations 7.2229924E-03 0.1465549 at 140iterations 4.1363332E-03 8.7249756E-02 at 150iterations 2.3699591E-03 4.4873238E-02 at 160iterations 1.3614245E-03 2.7207851E-02 at 170iterations 7.8052207E-04 1.4747620E-02 at 180iterations finished qdiffx linear iterations at : 16:25:36 total time elapsed so far: 15.49000 # loops : 180 mean,max change (kT/e) : 7.8052207E-04 1.4747620E-02 energy calculations done at 15.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.67000 DelPhi exited at 16:25:36 15.676u 0.296s 0:16.25 98.2% 0+0k 0+0io 0pf+0w