Mon Oct 10 17:02:36 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+sph.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 = amb.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 17:02:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2997 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5461714 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): -2.316000 62.86500 ymin,ymax (A): 13.78600 60.92800 zmin,zma (A): -9.405000 35.24100 x,y,z range (A): 65.18100 47.14200 44.64600 scale (grids/A): 0.5461714 object centre (A): 30.27450 37.35700 12.91800 number of atom coordinates read : 2997 total number of charged atoms : 2856 net assigned charge : -2.999976 assigned positive charge : 447.7580 centred at (gu) : 89.54920 90.22974 90.28792 assigned negative charge : -450.7591 centred at (gu) : 89.49112 90.37382 90.15940 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5738 nv = 96 ne = 84 npr = 60342 no. pairs analyzed = 60342 no. exposed pairs = 3929 no. arc points = 27763 no. surface atoms = 1316 nbur = 1681 mkacc time = 0.1100000 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 = 1.568000 m= 216 mr = 2863 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.2200000 number of dielectric boundary points 3079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2750 ## 364 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7540 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.9767439E-10 7.2490625E-10 midg,1,midg; midg,igrid,midg 7.3168327E-10 -1.2513096E-09 1,midg,midg; igrid,midg,midg -6.5144951E-10 1.8343693E-10 gauss-seidel spectral radius is 0.9827200 estimated iterations to convergence 63 setup time was (sec) 0.4000000 now iterating at: 17:02:36 rms-change max change #iterations 7.2641507E-02 18.33391 at 10iterations 4.7819801E-03 1.220612 at 20iterations 3.2138021E-04 6.2988281E-02 at 30iterations 2.1320917E-05 3.8700104E-03 at 40iterations 1.4323334E-06 2.4318695E-04 at 50iterations finished qdiffx linear iterations at : 17:02:39 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.4323334E-06 2.4318695E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 17:02:40 3.452u 0.171s 0:04.27 84.7% 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 17:02:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2997 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: 1.638514 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): -2.316000 62.86500 ymin,ymax (A): 13.78600 60.92800 zmin,zma (A): -9.405000 35.24100 x,y,z range (A): 65.18100 47.14200 44.64600 scale (grids/A): 1.638514 object centre (A): 30.27450 37.35700 12.91800 number of atom coordinates read : 2997 total number of charged atoms : 2856 net assigned charge : -2.999976 assigned positive charge : 447.7580 centred at (gu) : 88.64688 90.68830 90.86293 assigned negative charge : -450.7591 centred at (gu) : 88.47287 91.12115 90.47802 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63085 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27763 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18536 mr = 41589 m= 1801 mr = 12362 m= 43 mr = 847 m= 0 mr = 10 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 1082 time to turn everything in is 0.3000000 number of dielectric boundary points 28657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 298 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 21882 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) : 0.5461714 object centre at (A) : 30.27450 37.35700 12.91800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7862316E-03 4.7883145E-03 midg,1,midg; midg,igrid,midg 4.8808334E-03 -1.8612619E-02 1,midg,midg; igrid,midg,midg -2.2768948E-02 2.2942636E-03 gauss-seidel spectral radius is 0.9981980 estimated iterations to convergence 187 setup time was (sec) 0.5200000 now iterating at: 17:02:41 rms-change max change #iterations 3.357649 142.4098 at 10iterations 1.397575 58.71702 at 20iterations 0.5822024 21.46587 at 30iterations 0.2442133 10.28907 at 40iterations 0.1015932 4.170271 at 50iterations 4.2554401E-02 1.715457 at 60iterations 1.7737392E-02 0.6079288 at 70iterations 7.4334997E-03 0.2931595 at 80iterations 3.1030809E-03 0.1102562 at 90iterations 1.2953281E-03 5.0613403E-02 at 100iterations 5.4253632E-04 2.1621704E-02 at 110iterations 2.2650292E-04 8.7490082E-03 at 120iterations finished qdiffx linear iterations at : 17:02:48 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 2.2650292E-04 8.7490082E-03 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 17:02:48 7.523u 0.199s 0:08.30 92.8% 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 17:02:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2997 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.457772 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): -2.316000 62.86500 ymin,ymax (A): 13.78600 60.92800 zmin,zma (A): -9.405000 35.24100 x,y,z range (A): 65.18100 47.14200 44.64600 scale (grids/A): 2.457772 object centre (A): 30.27450 37.35700 12.91800 number of atom coordinates read : 2997 total number of charged atoms : 2856 net assigned charge : -2.999976 assigned positive charge : 447.7580 centred at (gu) : 87.97018 91.03217 91.29414 assigned negative charge : -450.7591 centred at (gu) : 87.70916 91.68169 90.71710 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 146836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27763 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 64591 mr = 102333 m= 17674 mr = 50001 m= 2658 mr = 13014 m= 160 mr = 1735 m= 2 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 3827 time to turn everything in is 0.7600000 number of dielectric boundary points 64762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 22817 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) : 1.638514 object centre at (A) : 30.27450 37.35700 12.91800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5712095E-02 6.2967271E-02 midg,1,midg; midg,igrid,midg 9.3474321E-02 -0.2710270 1,midg,midg; igrid,midg,midg -0.7458255 0.4289331 gauss-seidel spectral radius is 0.9991441 estimated iterations to convergence 270 setup time was (sec) 0.9800000 now iterating at: 17:02:50 rms-change max change #iterations 8.675931 297.2352 at 10iterations 4.845844 122.3892 at 20iterations 2.700494 60.59998 at 30iterations 1.502579 34.68335 at 40iterations 0.8309268 19.72015 at 50iterations 0.4585233 9.971619 at 60iterations 0.2532060 6.475288 at 70iterations 0.1400281 2.961805 at 80iterations 7.7086821E-02 1.642465 at 90iterations 4.2348940E-02 1.010414 at 100iterations 2.3288401E-02 0.4647465 at 110iterations 1.2854011E-02 0.2723389 at 120iterations 7.0597013E-03 0.1602726 at 130iterations 3.8877595E-03 8.0826044E-02 at 140iterations 2.1356011E-03 4.6660423E-02 at 150iterations 1.1759690E-03 2.6195526E-02 at 160iterations 6.4562022E-04 1.4586627E-02 at 170iterations 3.5489947E-04 7.5516701E-03 at 180iterations finished qdiffx linear iterations at : 17:03:01 total time elapsed so far: 11.93000 # loops : 180 mean,max change (kT/e) : 3.5489947E-04 7.5516701E-03 energy calculations done at 11.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.06000 DelPhi exited at 17:03:02 12.064u 0.201s 0:13.48 90.9% 0+0k 0+0io 0pf+0w