Wed Dec 28 11:03:02 PST 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 Wed Dec 28 2011 at 11:03:02 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6231947 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): -35.11300 10.02100 ymin,ymax (A): 1.131000 41.16700 zmin,zma (A): -1.747000 55.37800 x,y,z range (A): 45.13400 40.03600 57.12500 scale (grids/A): 0.6231947 object centre (A): -12.54600 21.14900 26.81550 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 4.000004 assigned positive charge : 291.4719 centred at (gu) : 90.39717 89.60541 90.65331 assigned negative charge : -287.4722 centred at (gu) : 90.35445 89.69037 90.67764 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5201 nv = 96 ne = 84 npr = 40662 no. pairs analyzed = 40662 no. exposed pairs = 2479 no. arc points = 17061 no. surface atoms = 840 nbur = 1126 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 246 mr = 2891 m= 0 mr = 26 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2530 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1693 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6134 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2073744E-09 2.5300508E-09 midg,1,midg; midg,igrid,midg 8.8013516E-09 -9.9369812E-10 1,midg,midg; igrid,midg,midg 1.1240194E-09 6.3490977E-09 gauss-seidel spectral radius is 0.9866084 estimated iterations to convergence 71 setup time was (sec) 0.6700000 now iterating at: 11:03:03 rms-change max change #iterations 0.1130568 19.18615 at 10iterations 1.0173302E-02 1.553116 at 20iterations 9.5966738E-04 0.1902695 at 30iterations 8.7929962E-05 1.3854980E-02 at 40iterations 8.2144115E-06 1.3066530E-03 at 50iterations finished qdiffx linear iterations at : 11:03:10 total time elapsed so far: 7.650000 # loops : 50 mean,max change (kT/e) : 8.2144115E-06 1.3066530E-03 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 11:03:11 7.820u 0.588s 0:08.97 93.6% 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 Wed Dec 28 2011 at 11:03:11 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.869584 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): -35.11300 10.02100 ymin,ymax (A): 1.131000 41.16700 zmin,zma (A): -1.747000 55.37800 x,y,z range (A): 45.13400 40.03600 57.12500 scale (grids/A): 1.869584 object centre (A): -12.54600 21.14900 26.81550 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 4.000004 assigned positive charge : 291.4719 centred at (gu) : 91.19147 88.81630 91.95997 assigned negative charge : -287.4722 centred at (gu) : 91.06346 89.07115 92.03307 start vw surface at 0.1000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 55780 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17061 grid for indexing accessible points = 1.400000 m= 20148 mr = 38587 m= 2828 mr = 15214 m= 138 mr = 1778 m= 2 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 230 time to turn everything in is 0.5300000 number of dielectric boundary points 23250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 14383 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) : 0.6231947 object centre at (A) : -12.54600 21.14900 26.81550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5981225E-02 3.6982987E-02 midg,1,midg; midg,igrid,midg 1.9222174E-03 -1.4371858E-03 1,midg,midg; igrid,midg,midg -1.1390398E-03 -1.5663792E-03 gauss-seidel spectral radius is 0.9985064 estimated iterations to convergence 205 setup time was (sec) 1.080000 now iterating at: 11:03:13 rms-change max change #iterations 3.487683 164.0930 at 10iterations 1.582976 59.94303 at 20iterations 0.7138741 25.76509 at 30iterations 0.3228704 12.00137 at 40iterations 0.1458746 5.069103 at 50iterations 6.5932781E-02 2.349789 at 60iterations 2.9874723E-02 1.195839 at 70iterations 1.3477921E-02 0.5521946 at 80iterations 6.0876515E-03 0.2336277 at 90iterations 2.7660318E-03 0.1098204 at 100iterations 1.2457117E-03 4.7045708E-02 at 110iterations 5.6488882E-04 2.0126343E-02 at 120iterations finished qdiffx linear iterations at : 11:03:29 total time elapsed so far: 16.54000 # loops : 120 mean,max change (kT/e) : 5.6488882E-04 2.0126343E-02 energy calculations done at 16.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.72000 DelPhi exited at 11:03:29 16.728u 0.833s 0:17.88 98.1% 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 Wed Dec 28 2011 at 11:03:29 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.804376 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): -35.11300 10.02100 ymin,ymax (A): 1.131000 41.16700 zmin,zma (A): -1.747000 55.37800 x,y,z range (A): 45.13400 40.03600 57.12500 scale (grids/A): 2.804376 object centre (A): -12.54600 21.14900 26.81550 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 4.000004 assigned positive charge : 291.4719 centred at (gu) : 91.78725 88.22439 92.93986 assigned negative charge : -287.4722 centred at (gu) : 91.59519 88.60676 93.04958 start vw surface at 0.1200000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 128823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17061 grid for indexing accessible points = 1.400000 m= 65845 mr = 93403 m= 23117 mr = 54451 m= 5026 mr = 18958 m= 579 mr = 3801 m= 32 mr = 422 m= 0 mr = 11 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 911 time to turn everything in is 1.370000 number of dielectric boundary points 52376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 14671 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) : 1.869584 object centre at (A) : -12.54600 21.14900 26.81550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1515795 0.3379506 midg,1,midg; midg,igrid,midg -4.3012124E-02 -1.3954980E-02 1,midg,midg; igrid,midg,midg -5.2142300E-02 -5.9856340E-02 gauss-seidel spectral radius is 0.9992049 estimated iterations to convergence 280 setup time was (sec) 1.910000 now iterating at: 11:03:32 rms-change max change #iterations 8.298936 342.5206 at 10iterations 4.758878 141.6879 at 20iterations 2.702222 64.83776 at 30iterations 1.527354 31.94007 at 40iterations 0.8610520 19.69760 at 50iterations 0.4855102 9.794907 at 60iterations 0.2741191 5.743411 at 70iterations 0.1539126 3.726505 at 80iterations 8.6935036E-02 1.785496 at 90iterations 4.8796270E-02 1.041986 at 100iterations 2.7430378E-02 0.5475330 at 110iterations 1.5459079E-02 0.3321009 at 120iterations 8.6630723E-03 0.1808968 at 130iterations 4.8689302E-03 0.1016974 at 140iterations 2.7361398E-03 5.7327747E-02 at 150iterations 1.5400964E-03 3.4066677E-02 at 160iterations 8.6503109E-04 1.8856049E-02 at 170iterations 4.8683191E-04 9.6168518E-03 at 180iterations finished qdiffx linear iterations at : 11:03:58 total time elapsed so far: 28.11000 # loops : 180 mean,max change (kT/e) : 4.8683191E-04 9.6168518E-03 energy calculations done at 28.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 28.30000 DelPhi exited at 11:03:59 28.300u 0.877s 0:29.58 98.6% 0+0k 0+0io 0pf+0w