Tue Oct 11 04:47:53 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 Tue Oct 11 2011 at 04:47:53 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2713 !!! WARNING: HIR 70 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6421704 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): -11.45800 36.87200 ymin,ymax (A): -26.08100 22.56900 zmin,zma (A): -10.19400 45.24300 x,y,z range (A): 48.33000 48.65000 55.43700 scale (grids/A): 0.6421704 object centre (A): 12.70700 -1.756000 17.52450 number of atom coordinates read : 2713 total number of charged atoms : 2564 net assigned charge : 1.514016 assigned positive charge : 414.0758 centred at (gu) : 90.05879 90.53146 92.14218 assigned negative charge : -412.5623 centred at (gu) : 89.82375 90.37454 92.04305 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7299 nv = 96 ne = 84 npr = 55644 no. pairs analyzed = 55644 no. exposed pairs = 3349 no. arc points = 23355 no. surface atoms = 1132 nbur = 1581 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 412 mr = 4042 m= 0 mr = 37 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3200000 number of dielectric boundary points 3632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2343 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8921 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0161850E-09 2.3613413E-08 midg,1,midg; midg,igrid,midg -1.6877372E-08 2.4846543E-08 1,midg,midg; igrid,midg,midg -2.9252503E-08 3.2352823E-08 gauss-seidel spectral radius is 0.9874403 estimated iterations to convergence 73 setup time was (sec) 0.5400000 now iterating at: 04:47:54 rms-change max change #iterations 0.1558257 21.94821 at 10iterations 1.5778881E-02 2.092118 at 20iterations 1.6480704E-03 0.2250729 at 30iterations 1.7821816E-04 2.8953552E-02 at 40iterations 2.4061190E-05 3.7832260E-03 at 50iterations finished qdiffx linear iterations at : 04:47:56 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 2.4061190E-05 3.7832260E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 04:47:57 3.133u 0.163s 0:03.63 90.6% 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 Tue Oct 11 2011 at 04:47:57 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2713 !!! WARNING: HIR 70 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.926511 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): -11.45800 36.87200 ymin,ymax (A): -26.08100 22.56900 zmin,zma (A): -10.19400 45.24300 x,y,z range (A): 48.33000 48.65000 55.43700 scale (grids/A): 1.926511 object centre (A): 12.70700 -1.756000 17.52450 number of atom coordinates read : 2713 total number of charged atoms : 2564 net assigned charge : 1.514016 assigned positive charge : 414.0758 centred at (gu) : 90.17584 91.59403 96.42591 assigned negative charge : -412.5623 centred at (gu) : 89.47099 91.12302 96.12900 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78726 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23355 grid for indexing accessible points = 1.400000 m= 28870 mr = 54923 m= 4346 mr = 21221 m= 243 mr = 2609 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 188 time to turn everything in is 0.5400000 number of dielectric boundary points 33375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 20178 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) : 0.6421704 object centre at (A) : 12.70700 -1.756000 17.52450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7920348E-02 5.3345938E-03 midg,1,midg; midg,igrid,midg -1.6148886E-02 1.9325791E-02 1,midg,midg; igrid,midg,midg -1.0633167E-02 5.0256617E-02 gauss-seidel spectral radius is 0.9986734 estimated iterations to convergence 218 setup time was (sec) 0.8100000 now iterating at: 04:47:58 rms-change max change #iterations 4.527777 194.9684 at 10iterations 2.144385 75.27525 at 20iterations 1.016371 30.68299 at 30iterations 0.4825826 16.22617 at 40iterations 0.2288577 7.789478 at 50iterations 0.1087187 3.149899 at 60iterations 5.1353566E-02 1.531086 at 70iterations 2.4516435E-02 0.7458649 at 80iterations 1.1594817E-02 0.3850727 at 90iterations 5.5048265E-03 0.1545830 at 100iterations 2.6167911E-03 7.8411102E-02 at 110iterations 1.2389937E-03 3.9112091E-02 at 120iterations finished qdiffx linear iterations at : 04:48:04 total time elapsed so far: 6.820000 # loops : 120 mean,max change (kT/e) : 1.2389937E-03 3.9112091E-02 energy calculations done at 6.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 04:48:05 7.008u 0.173s 0:07.82 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 Tue Oct 11 2011 at 04:48:05 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2713 !!! WARNING: HIR 70 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.889767 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): -11.45800 36.87200 ymin,ymax (A): -26.08100 22.56900 zmin,zma (A): -10.19400 45.24300 x,y,z range (A): 48.33000 48.65000 55.43700 scale (grids/A): 2.889767 object centre (A): 12.70700 -1.756000 17.52450 number of atom coordinates read : 2713 total number of charged atoms : 2564 net assigned charge : 1.514016 assigned positive charge : 414.0758 centred at (gu) : 90.26367 92.39085 99.63878 assigned negative charge : -412.5623 centred at (gu) : 89.20654 91.68454 99.19341 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 182027 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23355 grid for indexing accessible points = 1.400000 m= 92952 mr = 132761 m= 33561 mr = 76094 m= 7818 mr = 27019 m= 991 mr = 5682 m= 58 mr = 580 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 646 time to turn everything in is 1.380000 number of dielectric boundary points 75256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 20512 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) : 1.926511 object centre at (A) : 12.70700 -1.756000 17.52450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5413334 0.2464978 midg,1,midg; midg,igrid,midg -0.1918263 0.2048541 1,midg,midg; igrid,midg,midg -3.9438490E-02 0.4267368 gauss-seidel spectral radius is 0.9992678 estimated iterations to convergence 292 setup time was (sec) 1.650000 now iterating at: 04:48:07 rms-change max change #iterations 10.58941 400.2734 at 10iterations 6.212787 138.0616 at 20iterations 3.633668 83.52118 at 30iterations 2.122238 53.84573 at 40iterations 1.234763 27.89754 at 50iterations 0.7157962 13.29476 at 60iterations 0.4142638 7.662778 at 70iterations 0.2407845 4.317642 at 80iterations 0.1392244 2.619997 at 90iterations 8.0713086E-02 1.467255 at 100iterations 4.6686709E-02 0.8766110 at 110iterations 2.7060276E-02 0.4567842 at 120iterations 1.5611191E-02 0.2717438 at 130iterations 9.0571437E-03 0.1657219 at 140iterations 5.2507455E-03 0.1040802 at 150iterations 3.0601358E-03 5.6617737E-02 at 160iterations 1.7934992E-03 3.3676147E-02 at 170iterations 1.0616197E-03 1.9844055E-02 at 180iterations finished qdiffx linear iterations at : 04:48:16 total time elapsed so far: 11.13000 # loops : 180 mean,max change (kT/e) : 1.0616197E-03 1.9844055E-02 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.31000 DelPhi exited at 04:48:17 11.316u 0.175s 0:12.16 94.4% 0+0k 0+0io 0pf+0w