Thu Jan 19 13:35:21 PST 2012 #!/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 Thu Jan 19 2012 at 13:35:22 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: 393 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6776 !!! WARNING: HIR 58 has a net charge of 0.5220 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4357671 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): -3.382000 78.31300 ymin,ymax (A): -11.50600 65.99900 zmin,zma (A): 7.638999 74.15600 x,y,z range (A): 81.69501 77.50500 66.51700 scale (grids/A): 0.4357671 object centre (A): 37.46550 27.24650 40.89750 number of atom coordinates read : 6776 total number of charged atoms : 6601 net assigned charge : 0.6280531 assigned positive charge : 1033.139 centred at (gu) : 87.91045 90.35211 89.67425 assigned negative charge : -1032.521 centred at (gu) : 87.84068 90.41649 89.57197 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7529 nv = 96 ne = 84 npr = 137224 no. pairs analyzed = 137224 no. exposed pairs = 8874 no. arc points = 59716 no. surface atoms = 2967 nbur = 3809 mkacc time = 0.2300000 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 = 1.932000 m= 196 mr = 3548 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4968 ## 1006 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10442 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.6672288E-12 8.3415098E-12 midg,1,midg; midg,igrid,midg 5.3652941E-12 -5.9382113E-12 1,midg,midg; igrid,midg,midg -1.1192412E-11 3.4049434E-12 gauss-seidel spectral radius is 0.9732684 estimated iterations to convergence 51 setup time was (sec) 0.6400000 now iterating at: 13:35:26 rms-change max change #iterations 3.3893958E-02 7.152016 at 10iterations 1.7651381E-03 0.2705154 at 20iterations 4.9169367E-04 7.8549385E-02 at 30iterations 1.9437692E-04 3.0406952E-02 at 40iterations 7.8528174E-05 1.2033463E-02 at 50iterations finished qdiffx linear iterations at : 13:35:35 total time elapsed so far: 3.660000 # loops : 50 mean,max change (kT/e) : 7.8528174E-05 1.2033463E-02 energy calculations done at 3.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 13:35:37 3.784u 0.177s 0:15.43 25.5% 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 Thu Jan 19 2012 at 13:35:39 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: 393 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6776 !!! WARNING: HIR 58 has a net charge of 0.5220 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.307301 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): -3.382000 78.31300 ymin,ymax (A): -11.50600 65.99900 zmin,zma (A): 7.638999 74.15600 x,y,z range (A): 81.69501 77.50500 66.51700 scale (grids/A): 1.307301 object centre (A): 37.46550 27.24650 40.89750 number of atom coordinates read : 6776 total number of charged atoms : 6601 net assigned charge : 0.6280531 assigned positive charge : 1033.139 centred at (gu) : 83.72875 91.05407 89.02059 assigned negative charge : -1032.521 centred at (gu) : 83.52124 91.24940 88.71545 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 87084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 59716 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 20226 mr = 56851 m= 916 mr = 11977 m= 10 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 973 time to turn everything in is 0.4600000 number of dielectric boundary points 39227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1003 ## 35 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 46197 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) : 0.4357671 object centre at (A) : 37.46550 27.24650 40.89750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5633259E-03 2.5791659E-03 midg,1,midg; midg,igrid,midg 7.4085337E-03 1.8965352E-03 1,midg,midg; igrid,midg,midg -1.5611119E-02 1.6302913E-03 gauss-seidel spectral radius is 0.9974802 estimated iterations to convergence 159 setup time was (sec) 0.6800000 now iterating at: 13:35:44 rms-change max change #iterations 3.182588 141.9488 at 10iterations 1.136397 46.63914 at 20iterations 0.4064102 14.81980 at 30iterations 0.1452529 4.930141 at 40iterations 5.2183833E-02 1.795971 at 50iterations 1.8939782E-02 0.6653080 at 60iterations 7.1008434E-03 0.2624969 at 70iterations 2.9108101E-03 0.1101189 at 80iterations 1.4551234E-03 5.1038742E-02 at 90iterations 8.9658675E-04 3.0078888E-02 at 100iterations 6.1312324E-04 1.9527435E-02 at 110iterations 4.3447284E-04 1.3367653E-02 at 120iterations finished qdiffx linear iterations at : 13:36:06 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 4.3447284E-04 1.3367653E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 13:36:08 8.187u 0.219s 0:29.26 28.6% 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 Thu Jan 19 2012 at 13:36:09 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: 393 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6776 !!! WARNING: HIR 58 has a net charge of 0.5220 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.960952 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): -3.382000 78.31300 ymin,ymax (A): -11.50600 65.99900 zmin,zma (A): 7.638999 74.15600 x,y,z range (A): 81.69501 77.50500 66.51700 scale (grids/A): 1.960952 object centre (A): 37.46550 27.24650 40.89750 number of atom coordinates read : 6776 total number of charged atoms : 6601 net assigned charge : 0.6280531 assigned positive charge : 1033.139 centred at (gu) : 80.59272 91.58054 88.53050 assigned negative charge : -1032.521 centred at (gu) : 80.28165 91.87386 88.07309 start vw surface at 0.1700000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 204182 reading accessible surface arcs data from file ARCDAT no. of arc points read = 59716 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 78487 mr = 141761 m= 13604 mr = 57769 m= 928 mr = 8640 m= 12 mr = 317 m= 0 mr = 0 time to grow re-entrant surface = 0.5699999 no. cavity mid-points inaccessible to solvent = 3257 time to turn everything in is 1.060000 number of dielectric boundary points 88726 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 295 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 52140 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) : 1.307301 object centre at (A) : 37.46550 27.24650 40.89750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3419047E-02 6.7760900E-02 midg,1,midg; midg,igrid,midg 0.2284872 0.1367557 1,midg,midg; igrid,midg,midg -0.4395055 6.7117706E-02 gauss-seidel spectral radius is 0.9990060 estimated iterations to convergence 251 setup time was (sec) 1.330000 now iterating at: 13:36:11 rms-change max change #iterations 9.694360 248.0485 at 10iterations 5.284734 126.8761 at 20iterations 2.867339 69.46531 at 30iterations 1.539386 36.90410 at 40iterations 0.8261254 17.45024 at 50iterations 0.4410548 10.12338 at 60iterations 0.2348302 5.416402 at 70iterations 0.1247364 2.664958 at 80iterations 6.6222787E-02 1.477982 at 90iterations 3.5049934E-02 0.7329078 at 100iterations 1.8592253E-02 0.3871269 at 110iterations 9.8073613E-03 0.2341838 at 120iterations 5.1891580E-03 0.1071019 at 130iterations 2.7506591E-03 5.5770874E-02 at 140iterations 1.4667157E-03 3.0498981E-02 at 150iterations 7.8343478E-04 1.5910149E-02 at 160iterations 4.2759837E-04 9.3598366E-03 at 170iterations 2.4082650E-04 5.3424835E-03 at 180iterations finished qdiffx linear iterations at : 13:36:41 total time elapsed so far: 13.37000 # loops : 180 mean,max change (kT/e) : 2.4082650E-04 5.3424835E-03 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 13:36:42 13.503u 0.206s 0:32.82 41.7% 0+0k 0+0io 0pf+0w