Sat Oct 15 11:26:22 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 Sat Oct 15 2011 at 11:26:22 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 !!! WARNING: SEP 61 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6052465 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): -0.7270000 58.09200 ymin,ymax (A): -24.23900 26.94800 zmin,zma (A): -9.947001 45.00600 x,y,z range (A): 58.81900 51.18700 54.95300 scale (grids/A): 0.6052465 object centre (A): 28.68250 1.354500 17.52950 number of atom coordinates read : 3221 total number of charged atoms : 3073 net assigned charge : 5.025010 assigned positive charge : 481.8879 centred at (gu) : 91.78749 89.33896 90.00654 assigned negative charge : -476.8642 centred at (gu) : 91.81293 89.39739 89.95707 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7748 nv = 96 ne = 84 npr = 66476 no. pairs analyzed = 66476 no. exposed pairs = 3641 no. arc points = 25630 no. surface atoms = 1236 nbur = 1985 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 4448 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3637 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2585 ## 274 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9715 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4804363E-11 5.1341758E-09 midg,1,midg; midg,igrid,midg 6.4880195E-09 -4.4834456E-10 1,midg,midg; igrid,midg,midg 2.6189932E-09 1.7452141E-09 gauss-seidel spectral radius is 0.9859166 estimated iterations to convergence 69 setup time was (sec) 0.4200000 now iterating at: 11:26:22 rms-change max change #iterations 0.1264313 16.71332 at 10iterations 1.1154983E-02 1.502352 at 20iterations 1.0018965E-03 0.1761777 at 30iterations 9.5470998E-05 1.4431000E-02 at 40iterations 1.0706272E-05 1.5716553E-03 at 50iterations finished qdiffx linear iterations at : 11:26:25 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 1.0706272E-05 1.5716553E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 11:26:26 3.542u 0.182s 0:04.13 90.0% 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 Sat Oct 15 2011 at 11:26:26 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 !!! WARNING: SEP 61 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.815740 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): -0.7270000 58.09200 ymin,ymax (A): -24.23900 26.94800 zmin,zma (A): -9.947001 45.00600 x,y,z range (A): 58.81900 51.18700 54.95300 scale (grids/A): 1.815740 object centre (A): 28.68250 1.354500 17.52950 number of atom coordinates read : 3221 total number of charged atoms : 3073 net assigned charge : 5.025010 assigned positive charge : 481.8879 centred at (gu) : 95.36153 88.01614 90.01831 assigned negative charge : -476.8642 centred at (gu) : 95.43857 88.19162 89.87102 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 84422 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25630 grid for indexing accessible points = 1.400000 m= 29680 mr = 60027 m= 3969 mr = 22152 m= 154 mr = 2439 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1826 time to turn everything in is 0.4200000 number of dielectric boundary points 33571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 199 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 23984 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) : 0.6052465 object centre at (A) : 28.68250 1.354500 17.52950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1454788E-04 -1.2891359E-02 midg,1,midg; midg,igrid,midg 6.0361908E-03 4.7107055E-03 1,midg,midg; igrid,midg,midg 4.0225554E-02 2.7275233E-02 gauss-seidel spectral radius is 0.9985563 estimated iterations to convergence 209 setup time was (sec) 0.6400000 now iterating at: 11:26:27 rms-change max change #iterations 4.319544 162.1368 at 10iterations 1.978163 65.47945 at 20iterations 0.9079911 27.04243 at 30iterations 0.4162702 12.69709 at 40iterations 0.1909011 5.626997 at 50iterations 8.7790444E-02 2.714714 at 60iterations 4.0315416E-02 1.239532 at 70iterations 1.8514294E-02 0.5536069 at 80iterations 8.4893527E-03 0.2877769 at 90iterations 3.9181197E-03 0.1179347 at 100iterations 1.7922844E-03 5.3375244E-02 at 110iterations 8.2200294E-04 2.3305893E-02 at 120iterations finished qdiffx linear iterations at : 11:26:37 total time elapsed so far: 9.700000 # loops : 120 mean,max change (kT/e) : 8.2200294E-04 2.3305893E-02 energy calculations done at 9.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.840000 DelPhi exited at 11:26:39 9.838u 0.237s 0:12.85 78.2% 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 15 2011 at 11:26:39 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 !!! WARNING: SEP 61 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.723609 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): -0.7270000 58.09200 ymin,ymax (A): -24.23900 26.94800 zmin,zma (A): -9.947001 45.00600 x,y,z range (A): 58.81900 51.18700 54.95300 scale (grids/A): 2.723609 object centre (A): 28.68250 1.354500 17.52950 number of atom coordinates read : 3221 total number of charged atoms : 3073 net assigned charge : 5.025010 assigned positive charge : 481.8879 centred at (gu) : 98.04207 87.02422 90.02725 assigned negative charge : -476.8642 centred at (gu) : 98.15791 87.28732 89.80640 start vw surface at 0.1000000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 195368 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25630 grid for indexing accessible points = 1.400000 m= 98251 mr = 145265 m= 33815 mr = 81251 m= 7021 mr = 27332 m= 734 mr = 5162 m= 19 mr = 440 m= 0 mr = 5 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 6460 time to turn everything in is 1.220000 number of dielectric boundary points 75753 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 24576 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) : 1.815740 object centre at (A) : 28.68250 1.354500 17.52950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9692672E-02 -0.2235897 midg,1,midg; midg,igrid,midg -4.3959036E-02 7.0723824E-02 1,midg,midg; igrid,midg,midg 0.4827225 0.3461796 gauss-seidel spectral radius is 0.9992489 estimated iterations to convergence 288 setup time was (sec) 1.610000 now iterating at: 11:26:41 rms-change max change #iterations 10.33766 288.4412 at 10iterations 6.002134 121.3643 at 20iterations 3.472219 68.38499 at 30iterations 1.993212 38.49057 at 40iterations 1.149204 20.52398 at 50iterations 0.6583762 11.10655 at 60iterations 0.3783332 7.177777 at 70iterations 0.2168985 3.707333 at 80iterations 0.1241264 2.179708 at 90iterations 7.1306400E-02 1.231819 at 100iterations 4.0733129E-02 0.7016726 at 110iterations 2.3303708E-02 0.4298838 at 120iterations 1.3347110E-02 0.2384291 at 130iterations 7.6483339E-03 0.1352613 at 140iterations 4.3792487E-03 7.6461792E-02 at 150iterations 2.5080529E-03 4.6543121E-02 at 160iterations 1.4347661E-03 2.6189804E-02 at 170iterations 8.2245655E-04 1.4593124E-02 at 180iterations finished qdiffx linear iterations at : 11:26:59 total time elapsed so far: 16.74000 # loops : 180 mean,max change (kT/e) : 8.2245655E-04 1.4593124E-02 energy calculations done at 16.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.87000 DelPhi exited at 11:27:00 16.872u 0.413s 0:21.24 81.3% 0+0k 0+0io 0pf+0w