Mon Oct 10 14:42:28 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 Mon Oct 10 2011 at 14:42:28 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5001 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.5209782 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): 7.447999 62.56400 ymin,ymax (A): -28.92400 39.40900 zmin,zma (A): -29.03800 33.57500 x,y,z range (A): 55.11600 68.33300 62.61300 scale (grids/A): 0.5209782 object centre (A): 35.00600 5.242500 2.268500 number of atom coordinates read : 5001 total number of charged atoms : 4837 net assigned charge : 0.9340141 assigned positive charge : 752.2853 centred at (gu) : 89.68440 89.37366 89.12215 assigned negative charge : -751.3560 centred at (gu) : 89.65009 89.37100 89.13348 start vw surface at 0.2300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 8560 nv = 96 ne = 84 npr = 102699 no. pairs analyzed = 102699 no. exposed pairs = 6128 no. arc points = 40858 no. surface atoms = 2067 nbur = 2934 mkacc time = 0.3500000 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 = 1.624000 m= 331 mr = 4654 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 4229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4096 ## 548 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 11558 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6197223E-11 -2.1206212E-11 midg,1,midg; midg,igrid,midg 1.1280353E-11 2.7364163E-11 1,midg,midg; igrid,midg,midg -1.3515451E-10 1.5177426E-10 gauss-seidel spectral radius is 0.9811658 estimated iterations to convergence 60 setup time was (sec) 0.9900000 now iterating at: 14:42:30 rms-change max change #iterations 7.8871675E-02 12.84946 at 10iterations 5.0964500E-03 0.9105721 at 20iterations 8.5049961E-04 0.1307907 at 30iterations 3.2652693E-04 4.0891647E-02 at 40iterations 1.4074655E-04 1.8243790E-02 at 50iterations finished qdiffx linear iterations at : 14:42:34 total time elapsed so far: 4.860000 # loops : 50 mean,max change (kT/e) : 1.4074655E-04 1.8243790E-02 energy calculations done at 4.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.070000 DelPhi exited at 14:42:35 5.074u 0.451s 0:06.97 79.1% 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 Mon Oct 10 2011 at 14:42:35 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5001 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.562934 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): 7.447999 62.56400 ymin,ymax (A): -28.92400 39.40900 zmin,zma (A): -29.03800 33.57500 x,y,z range (A): 55.11600 68.33300 62.61300 scale (grids/A): 1.562934 object centre (A): 35.00600 5.242500 2.268500 number of atom coordinates read : 5001 total number of charged atoms : 4837 net assigned charge : 0.9340141 assigned positive charge : 752.2853 centred at (gu) : 89.05152 88.11926 87.36489 assigned negative charge : -751.3560 centred at (gu) : 88.94980 88.11280 87.40001 start vw surface at 0.2300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 97133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40858 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 30246 mr = 68608 m= 2898 mr = 20822 m= 60 mr = 1422 m= 0 mr = 2 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 978 time to turn everything in is 1.050000 number of dielectric boundary points 39483 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 503 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 36582 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) : 0.5209782 object centre at (A) : 35.00600 5.242500 2.268500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9615675E-04 -1.3626217E-02 midg,1,midg; midg,igrid,midg 1.7592190E-02 -4.3203430E-03 1,midg,midg; igrid,midg,midg 2.3541351E-04 4.5225620E-03 gauss-seidel spectral radius is 0.9982117 estimated iterations to convergence 188 setup time was (sec) 1.400000 now iterating at: 14:42:37 rms-change max change #iterations 4.106071 161.3467 at 10iterations 1.717115 54.24495 at 20iterations 0.7230967 22.83682 at 30iterations 0.3026046 9.241741 at 40iterations 0.1275893 3.750128 at 50iterations 5.3801622E-02 1.793701 at 60iterations 2.2643324E-02 0.7129841 at 70iterations 9.6364627E-03 0.2852497 at 80iterations 4.2076600E-03 0.1401215 at 90iterations 1.9053248E-03 5.8982849E-02 at 100iterations 9.5707132E-04 2.9047012E-02 at 110iterations 5.5993110E-04 1.6925812E-02 at 120iterations finished qdiffx linear iterations at : 14:42:47 total time elapsed so far: 11.36000 # loops : 120 mean,max change (kT/e) : 5.5993110E-04 1.6925812E-02 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.58000 DelPhi exited at 14:42:48 11.588u 0.501s 0:12.43 97.1% 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 Mon Oct 10 2011 at 14:42:48 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5001 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.344402 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): 7.447999 62.56400 ymin,ymax (A): -28.92400 39.40900 zmin,zma (A): -29.03800 33.57500 x,y,z range (A): 55.11600 68.33300 62.61300 scale (grids/A): 2.344402 object centre (A): 35.00600 5.242500 2.268500 number of atom coordinates read : 5001 total number of charged atoms : 4837 net assigned charge : 0.9340141 assigned positive charge : 752.2853 centred at (gu) : 88.57687 87.17857 86.04681 assigned negative charge : -751.3560 centred at (gu) : 88.42453 87.16908 86.09988 start vw surface at 0.2300000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 226579 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40858 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 105424 mr = 168443 m= 29160 mr = 83536 m= 4353 mr = 21852 m= 231 mr = 2786 m= 4 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 1.530000 no. cavity mid-points inaccessible to solvent = 3445 time to turn everything in is 2.460000 number of dielectric boundary points 89038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 2.640000 number of grid points assigned charge 38611 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) : 1.562934 object centre at (A) : 35.00600 5.242500 2.268500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3176916E-02 -0.3387960 midg,1,midg; midg,igrid,midg 0.4715899 -0.1630542 1,midg,midg; igrid,midg,midg 5.7513930E-02 0.1166424 gauss-seidel spectral radius is 0.9991959 estimated iterations to convergence 278 setup time was (sec) 2.850000 now iterating at: 14:42:51 rms-change max change #iterations 10.97139 270.7867 at 10iterations 6.382703 170.3685 at 20iterations 3.693215 72.14282 at 30iterations 2.122528 60.65306 at 40iterations 1.214400 23.81559 at 50iterations 0.6907703 13.70386 at 60iterations 0.3929482 6.843599 at 70iterations 0.2228836 4.019091 at 80iterations 0.1260362 2.426715 at 90iterations 7.1449555E-02 1.208397 at 100iterations 4.0325165E-02 0.6753082 at 110iterations 2.2765858E-02 0.4197931 at 120iterations 1.2910963E-02 0.2411823 at 130iterations 7.3488131E-03 0.1264868 at 140iterations 4.2082765E-03 8.5807800E-02 at 150iterations 2.4558657E-03 4.1275024E-02 at 160iterations 1.4834959E-03 2.6054382E-02 at 170iterations 9.4092730E-04 1.7551422E-02 at 180iterations finished qdiffx linear iterations at : 14:43:08 total time elapsed so far: 20.03000 # loops : 180 mean,max change (kT/e) : 9.4092730E-04 1.7551422E-02 energy calculations done at 20.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.25000 DelPhi exited at 14:43:09 20.257u 0.535s 0:21.24 97.8% 0+0k 0+0io 0pf+0w