Sun Oct 9 10:57:33 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 Sun Oct 9 2011 at 10:57:33 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2615 !!! WARNING: HIR 215 has a net charge of 0.5140 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: 0.6045169 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): -21.82300 37.06700 ymin,ymax (A): 18.63300 75.75800 zmin,zma (A): 36.18900 88.57100 x,y,z range (A): 58.89000 57.12500 52.38200 scale (grids/A): 0.6045169 object centre (A): 7.621999 47.19550 62.38000 number of atom coordinates read : 2615 total number of charged atoms : 2472 net assigned charge : -7.485968 assigned positive charge : 376.8265 centred at (gu) : 90.04450 86.97190 89.92969 assigned negative charge : -384.3138 centred at (gu) : 90.11919 87.16013 90.13935 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6592 nv = 96 ne = 84 npr = 52189 no. pairs analyzed = 52189 no. exposed pairs = 3598 no. arc points = 25447 no. surface atoms = 1209 nbur = 1406 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 347 mr = 3302 m= 4 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2408 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7979 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5723647E-09 -1.2553329E-08 midg,1,midg; midg,igrid,midg 7.6832567E-09 -6.0396013E-09 1,midg,midg; igrid,midg,midg -8.6919716E-10 -7.0898536E-09 gauss-seidel spectral radius is 0.9858525 estimated iterations to convergence 69 setup time was (sec) 0.3800000 now iterating at: 10:57:34 rms-change max change #iterations 0.1099344 17.73636 at 10iterations 9.5230564E-03 1.707500 at 20iterations 8.2173903E-04 0.1153889 at 30iterations 7.5531243E-05 1.1810303E-02 at 40iterations 9.5432033E-06 1.8749237E-03 at 50iterations finished qdiffx linear iterations at : 10:57:37 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 9.5432033E-06 1.8749237E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 10:57:37 3.359u 0.170s 0:03.97 88.6% 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 Sun Oct 9 2011 at 10:57:37 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2615 !!! WARNING: HIR 215 has a net charge of 0.5140 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: 1.813551 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): -21.82300 37.06700 ymin,ymax (A): 18.63300 75.75800 zmin,zma (A): 36.18900 88.57100 x,y,z range (A): 58.89000 57.12500 52.38200 scale (grids/A): 1.813551 object centre (A): 7.621999 47.19550 62.38000 number of atom coordinates read : 2615 total number of charged atoms : 2472 net assigned charge : -7.485968 assigned positive charge : 376.8265 centred at (gu) : 90.13299 80.91534 89.78844 assigned negative charge : -384.3138 centred at (gu) : 90.35757 81.48035 90.41792 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 71481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25447 grid for indexing accessible points = 1.400000 m= 23979 mr = 47232 m= 3632 mr = 16674 m= 194 mr = 2109 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 664 time to turn everything in is 0.3500000 number of dielectric boundary points 33227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19378 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) : 0.6045169 object centre at (A) : 7.621999 47.19550 62.38000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0966113E-02 -3.6903515E-02 midg,1,midg; midg,igrid,midg 1.9384252E-02 -4.7655508E-02 1,midg,midg; igrid,midg,midg -2.1031605E-02 -2.7773540E-02 gauss-seidel spectral radius is 0.9985182 estimated iterations to convergence 206 setup time was (sec) 0.5700000 now iterating at: 10:57:38 rms-change max change #iterations 3.806707 169.8378 at 10iterations 1.715809 66.63373 at 20iterations 0.7753441 26.53392 at 30iterations 0.3528976 12.09242 at 40iterations 0.1587930 5.533989 at 50iterations 7.2187856E-02 2.381196 at 60iterations 3.2648172E-02 1.034898 at 70iterations 1.4817212E-02 0.4776847 at 80iterations 6.7512072E-03 0.2199402 at 90iterations 3.0491475E-03 0.1135979 at 100iterations 1.3815382E-03 4.4473648E-02 at 110iterations 6.3056179E-04 2.1667480E-02 at 120iterations finished qdiffx linear iterations at : 10:57:45 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 6.3056179E-04 2.1667480E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 10:57:46 7.725u 0.184s 0:08.48 93.1% 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 Sun Oct 9 2011 at 10:57:46 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2615 !!! WARNING: HIR 215 has a net charge of 0.5140 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: 2.720326 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): -21.82300 37.06700 ymin,ymax (A): 18.63300 75.75800 zmin,zma (A): 36.18900 88.57100 x,y,z range (A): 58.89000 57.12500 52.38200 scale (grids/A): 2.720326 object centre (A): 7.621999 47.19550 62.38000 number of atom coordinates read : 2615 total number of charged atoms : 2472 net assigned charge : -7.485968 assigned positive charge : 376.8265 centred at (gu) : 90.19928 76.37287 89.68253 assigned negative charge : -384.3138 centred at (gu) : 90.53611 77.22041 90.62681 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 165431 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25447 grid for indexing accessible points = 1.400000 m= 77904 mr = 115640 m= 27289 mr = 61165 m= 6393 mr = 21048 m= 816 mr = 4493 m= 37 mr = 468 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 2186 time to turn everything in is 0.9000000 number of dielectric boundary points 75047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 19773 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) : 1.813551 object centre at (A) : 7.621999 47.19550 62.38000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2679043 -0.3629675 midg,1,midg; midg,igrid,midg 0.3073677 -0.7278482 1,midg,midg; igrid,midg,midg -0.3453527 -0.2990161 gauss-seidel spectral radius is 0.9992365 estimated iterations to convergence 286 setup time was (sec) 1.140000 now iterating at: 10:57:47 rms-change max change #iterations 9.343347 304.7445 at 10iterations 5.475093 133.6152 at 20iterations 3.170587 64.19263 at 30iterations 1.829841 36.48188 at 40iterations 1.054346 20.60365 at 50iterations 0.6055962 11.97669 at 60iterations 0.3466719 6.489192 at 70iterations 0.1984768 3.919519 at 80iterations 0.1133085 2.189226 at 90iterations 6.4675771E-02 1.253376 at 100iterations 3.6968574E-02 0.6673794 at 110iterations 2.1034049E-02 0.4060059 at 120iterations 1.2010304E-02 0.2253146 at 130iterations 6.8446579E-03 0.1288390 at 140iterations 3.9046363E-03 7.3492765E-02 at 150iterations 2.2276028E-03 4.0734291E-02 at 160iterations 1.2669015E-03 2.3463249E-02 at 170iterations 7.2510401E-04 1.3188601E-02 at 180iterations finished qdiffx linear iterations at : 10:57:58 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 7.2510401E-04 1.3188601E-02 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 10:57:59 12.480u 0.199s 0:13.26 95.5% 0+0k 0+0io 0pf+0w