Sun Oct 9 16:30:53 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 Sun Oct 9 2011 at 16:30:53 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3006 !!! WARNING: GLM 48 has a net charge of -0.0940 !!! WARNING: GLM 120 has a net charge of -0.0940 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: 0.6148532 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): 8.356000 63.83400 ymin,ymax (A): -22.16700 35.73300 zmin,zma (A): -20.89700 32.52000 x,y,z range (A): 55.47800 57.90000 53.41700 scale (grids/A): 0.6148532 object centre (A): 36.09500 6.783001 5.811500 number of atom coordinates read : 3006 total number of charged atoms : 2920 net assigned charge : 1.812005 assigned positive charge : 459.0439 centred at (gu) : 90.14429 90.98802 91.36194 assigned negative charge : -457.2335 centred at (gu) : 90.04543 91.00368 91.25637 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7682 nv = 96 ne = 84 npr = 57930 no. pairs analyzed = 57930 no. exposed pairs = 4183 no. arc points = 29071 no. surface atoms = 1393 nbur = 1613 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 392 mr = 3892 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3900000 number of dielectric boundary points 4141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2869 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9516 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4329336E-09 1.1092346E-08 midg,1,midg; midg,igrid,midg 1.7661163E-09 8.9704980E-11 1,midg,midg; igrid,midg,midg -5.3958904E-09 7.9634992E-09 gauss-seidel spectral radius is 0.9863480 estimated iterations to convergence 70 setup time was (sec) 0.6700000 now iterating at: 16:30:54 rms-change max change #iterations 0.1334040 21.43379 at 10iterations 1.1979271E-02 1.728537 at 20iterations 1.1386267E-03 0.1574574 at 30iterations 1.4565446E-04 2.2842407E-02 at 40iterations 3.3021741E-05 5.6743622E-03 at 50iterations finished qdiffx linear iterations at : 16:30:57 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 3.3021741E-05 5.6743622E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 16:30:58 4.267u 0.257s 0:04.80 93.9% 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 16:30:58 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3006 !!! WARNING: GLM 48 has a net charge of -0.0940 !!! WARNING: GLM 120 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.844560 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): 8.356000 63.83400 ymin,ymax (A): -22.16700 35.73300 zmin,zma (A): -20.89700 32.52000 x,y,z range (A): 55.47800 57.90000 53.41700 scale (grids/A): 1.844560 object centre (A): 36.09500 6.783001 5.811500 number of atom coordinates read : 3006 total number of charged atoms : 2920 net assigned charge : 1.812005 assigned positive charge : 459.0439 centred at (gu) : 90.43196 92.96344 94.08495 assigned negative charge : -457.2335 centred at (gu) : 90.13615 93.01064 93.76868 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 82100 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29071 grid for indexing accessible points = 1.400000 m= 28795 mr = 54389 m= 4470 mr = 20260 m= 271 mr = 2740 m= 5 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 307 time to turn everything in is 0.7400000 number of dielectric boundary points 38175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 22831 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) : 0.6148532 object centre at (A) : 36.09500 6.783001 5.811500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7828738E-02 -4.1464823E-03 midg,1,midg; midg,igrid,midg 3.8684711E-02 3.0548528E-02 1,midg,midg; igrid,midg,midg -1.9809809E-02 -6.3622980E-03 gauss-seidel spectral radius is 0.9986002 estimated iterations to convergence 212 setup time was (sec) 1.080000 now iterating at: 16:30:59 rms-change max change #iterations 4.404507 166.1330 at 10iterations 2.040994 70.86247 at 20iterations 0.9482903 30.51532 at 30iterations 0.4406721 14.41718 at 40iterations 0.2040640 6.039475 at 50iterations 9.4864480E-02 3.494654 at 60iterations 4.4072762E-02 1.408607 at 70iterations 2.0407032E-02 0.6228018 at 80iterations 9.4886757E-03 0.2944150 at 90iterations 4.4154311E-03 0.1550198 at 100iterations 2.0490142E-03 6.2616825E-02 at 110iterations 9.5536589E-04 3.1099319E-02 at 120iterations finished qdiffx linear iterations at : 16:31:08 total time elapsed so far: 9.920000 # loops : 120 mean,max change (kT/e) : 9.5536589E-04 3.1099319E-02 energy calculations done at 9.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.14000 DelPhi exited at 16:31:09 10.147u 0.299s 0:10.73 97.2% 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 Sun Oct 9 2011 at 16:31:09 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3006 !!! WARNING: GLM 48 has a net charge of -0.0940 !!! WARNING: GLM 120 has a net charge of -0.0940 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: 2.766839 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): 8.356000 63.83400 ymin,ymax (A): -22.16700 35.73300 zmin,zma (A): -20.89700 32.52000 x,y,z range (A): 55.47800 57.90000 53.41700 scale (grids/A): 2.766839 object centre (A): 36.09500 6.783001 5.811500 number of atom coordinates read : 3006 total number of charged atoms : 2920 net assigned charge : 1.812005 assigned positive charge : 459.0439 centred at (gu) : 90.64771 94.44492 96.12737 assigned negative charge : -457.2335 centred at (gu) : 90.20423 94.51578 95.65289 start vw surface at 0.1900000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 190095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29071 grid for indexing accessible points = 1.400000 m= 92459 mr = 133178 m= 33139 mr = 73071 m= 7989 mr = 25914 m= 1031 mr = 5929 m= 54 mr = 670 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 1089 time to turn everything in is 1.680000 number of dielectric boundary points 85976 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 23356 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) : 1.844560 object centre at (A) : 36.09500 6.783001 5.811500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2374102 -0.1143887 midg,1,midg; midg,igrid,midg 0.3582499 0.4743487 1,midg,midg; igrid,midg,midg -0.2657848 -0.2542022 gauss-seidel spectral radius is 0.9992731 estimated iterations to convergence 293 setup time was (sec) 2.020000 now iterating at: 16:31:11 rms-change max change #iterations 10.62940 301.8624 at 10iterations 6.318073 155.8390 at 20iterations 3.730226 95.24962 at 30iterations 2.185992 42.70361 at 40iterations 1.276182 24.57159 at 50iterations 0.7445905 16.35295 at 60iterations 0.4329536 9.183627 at 70iterations 0.2513311 4.588335 at 80iterations 0.1459229 2.592279 at 90iterations 8.4466890E-02 1.425819 at 100iterations 4.8945926E-02 0.9353790 at 110iterations 2.8346613E-02 0.5010262 at 120iterations 1.6412821E-02 0.2896500 at 130iterations 9.4731981E-03 0.1696053 at 140iterations 5.4632551E-03 0.1054878 at 150iterations 3.1663165E-03 6.4867496E-02 at 160iterations 1.8303626E-03 3.4006119E-02 at 170iterations 1.0588403E-03 1.7990112E-02 at 180iterations finished qdiffx linear iterations at : 16:31:25 total time elapsed so far: 15.65000 # loops : 180 mean,max change (kT/e) : 1.0588403E-03 1.7990112E-02 energy calculations done at 15.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.89000 DelPhi exited at 16:31:25 15.888u 0.307s 0:16.47 98.2% 0+0k 0+0io 0pf+0w