Sun Oct 9 22:35:46 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 22:35:46 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3572 !!! WARNING: SEP 139 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5522719 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): -25.04400 28.48300 ymin,ymax (A): -31.52000 24.84100 zmin,zma (A): -78.97100 -14.51000 x,y,z range (A): 53.52700 56.36100 64.46100 scale (grids/A): 0.5522719 object centre (A): 1.719501 -3.339500 -46.74050 number of atom coordinates read : 3572 total number of charged atoms : 3420 net assigned charge : 7.525016 assigned positive charge : 548.5884 centred at (gu) : 89.55530 89.45192 89.79038 assigned negative charge : -541.0656 centred at (gu) : 89.61482 89.47636 89.69850 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7161 nv = 96 ne = 84 npr = 67918 no. pairs analyzed = 67918 no. exposed pairs = 4770 no. arc points = 35401 no. surface atoms = 1587 nbur = 1985 mkacc time = 0.1500000 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 = 1.568000 m= 298 mr = 3405 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3500000 number of dielectric boundary points 4049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3599 ## 499 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9399 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7344988E-10 1.4474230E-09 midg,1,midg; midg,igrid,midg 9.6450992E-10 3.0501840E-10 1,midg,midg; igrid,midg,midg 1.3367407E-09 -1.1747824E-11 gauss-seidel spectral radius is 0.9831554 estimated iterations to convergence 63 setup time was (sec) 0.5700000 now iterating at: 22:35:47 rms-change max change #iterations 8.7682188E-02 14.58247 at 10iterations 5.9065828E-03 1.090836 at 20iterations 4.0648109E-04 6.1452866E-02 at 30iterations 2.7941114E-05 4.3783188E-03 at 40iterations 2.1522221E-06 3.1185150E-04 at 50iterations finished qdiffx linear iterations at : 22:35:49 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 2.1522221E-06 3.1185150E-04 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 22:35:50 3.170u 0.140s 0:03.61 91.6% 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 22:35:50 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3572 !!! WARNING: SEP 139 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.656816 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): -25.04400 28.48300 ymin,ymax (A): -31.52000 24.84100 zmin,zma (A): -78.97100 -14.51000 x,y,z range (A): 53.52700 56.36100 64.46100 scale (grids/A): 1.656816 object centre (A): 1.719501 -3.339500 -46.74050 number of atom coordinates read : 3572 total number of charged atoms : 3420 net assigned charge : 7.525016 assigned positive charge : 548.5884 centred at (gu) : 88.66444 88.35468 89.37022 assigned negative charge : -541.0656 centred at (gu) : 88.84406 88.42869 89.09489 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79237 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35401 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22542 mr = 50868 m= 2360 mr = 14617 m= 78 mr = 1113 m= 0 mr = 6 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2376 time to turn everything in is 0.5200000 number of dielectric boundary points 37613 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 404 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 26265 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) : 0.5522719 object centre at (A) : 1.719501 -3.339500 -46.74050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7610715E-03 1.8383732E-02 midg,1,midg; midg,igrid,midg 8.6392062E-03 -4.4951579E-03 1,midg,midg; igrid,midg,midg 1.6120886E-02 1.0171516E-02 gauss-seidel spectral radius is 0.9983332 estimated iterations to convergence 194 setup time was (sec) 0.7800000 now iterating at: 22:35:50 rms-change max change #iterations 3.833593 164.2437 at 10iterations 1.646560 62.05160 at 20iterations 0.7089801 24.32515 at 30iterations 0.3045754 10.20997 at 40iterations 0.1314885 4.415627 at 50iterations 5.6689829E-02 1.910524 at 60iterations 2.4465250E-02 0.8255463 at 70iterations 1.0551141E-02 0.3923273 at 80iterations 4.5492984E-03 0.1517048 at 90iterations 1.9726169E-03 6.7320824E-02 at 100iterations 8.5065514E-04 2.9136658E-02 at 110iterations 3.6832798E-04 1.2901306E-02 at 120iterations finished qdiffx linear iterations at : 22:35:57 total time elapsed so far: 6.920000 # loops : 120 mean,max change (kT/e) : 3.6832798E-04 1.2901306E-02 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.110000 DelPhi exited at 22:35:57 7.117u 0.186s 0:07.59 96.0% 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 22:35:57 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3572 !!! WARNING: SEP 139 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.485224 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): -25.04400 28.48300 ymin,ymax (A): -31.52000 24.84100 zmin,zma (A): -78.97100 -14.51000 x,y,z range (A): 53.52700 56.36100 64.46100 scale (grids/A): 2.485224 object centre (A): 1.719501 -3.339500 -46.74050 number of atom coordinates read : 3572 total number of charged atoms : 3420 net assigned charge : 7.525016 assigned positive charge : 548.5884 centred at (gu) : 87.99644 87.53169 89.05506 assigned negative charge : -541.0656 centred at (gu) : 88.26607 87.64309 88.64221 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 184026 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35401 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 79143 mr = 125403 m= 21598 mr = 60537 m= 3733 mr = 15506 m= 301 mr = 2330 m= 2 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 7823 time to turn everything in is 1.250000 number of dielectric boundary points 84895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 27333 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) : 1.656816 object centre at (A) : 1.719501 -3.339500 -46.74050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3108319E-02 0.2913522 midg,1,midg; midg,igrid,midg 0.1522034 -9.8511994E-02 1,midg,midg; igrid,midg,midg 0.2610784 0.1550707 gauss-seidel spectral radius is 0.9992099 estimated iterations to convergence 281 setup time was (sec) 1.540000 now iterating at: 22:35:59 rms-change max change #iterations 9.895662 367.2307 at 10iterations 5.773275 144.8605 at 20iterations 3.328817 84.20779 at 30iterations 1.904564 37.11058 at 40iterations 1.088334 22.92400 at 50iterations 0.6195486 13.09237 at 60iterations 0.3521948 7.138382 at 70iterations 0.1997084 4.004181 at 80iterations 0.1131318 2.086262 at 90iterations 6.4091899E-02 1.376385 at 100iterations 3.6245827E-02 0.6578410 at 110iterations 2.0484339E-02 0.3753548 at 120iterations 1.1542699E-02 0.2028561 at 130iterations 6.5280157E-03 0.1226134 at 140iterations 3.6820201E-03 6.7758083E-02 at 150iterations 2.0804037E-03 3.7636757E-02 at 160iterations 1.1710603E-03 2.2655487E-02 at 170iterations 6.6184934E-04 1.1756897E-02 at 180iterations finished qdiffx linear iterations at : 22:36:09 total time elapsed so far: 11.30000 # loops : 180 mean,max change (kT/e) : 6.6184934E-04 1.1756897E-02 energy calculations done at 11.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.47000 DelPhi exited at 22:36:09 11.474u 0.208s 0:12.05 96.8% 0+0k 0+0io 0pf+0w