Tue Oct 11 03:41:15 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 Tue Oct 11 2011 at 03:41:15 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3086 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6574816 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): -11.77000 37.21900 ymin,ymax (A): -27.26200 21.56200 zmin,zma (A): -8.514999 45.63100 x,y,z range (A): 48.98900 48.82400 54.14600 scale (grids/A): 0.6574816 object centre (A): 12.72450 -2.849999 18.55800 number of atom coordinates read : 3086 total number of charged atoms : 2682 net assigned charge : -0.8379797 assigned positive charge : 426.3576 centred at (gu) : 90.11981 90.70813 91.36987 assigned negative charge : -427.1962 centred at (gu) : 89.87687 90.63168 91.28812 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8290 nv = 96 ne = 84 npr = 57573 no. pairs analyzed = 57573 no. exposed pairs = 3413 no. arc points = 23885 no. surface atoms = 1149 nbur = 1937 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 506 mr = 4796 m= 6 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.3400000 number of dielectric boundary points 3931 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2261 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9680 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4362377E-08 1.9052381E-08 midg,1,midg; midg,igrid,midg -1.5550253E-08 1.5262595E-08 1,midg,midg; igrid,midg,midg -5.1822884E-08 4.7082857E-08 gauss-seidel spectral radius is 0.9880295 estimated iterations to convergence 75 setup time was (sec) 0.5700000 now iterating at: 03:41:16 rms-change max change #iterations 0.1702033 22.51631 at 10iterations 1.8421963E-02 2.378184 at 20iterations 1.9787953E-03 0.2489455 at 30iterations 2.0954500E-04 2.9476643E-02 at 40iterations 2.4747964E-05 3.7441254E-03 at 50iterations finished qdiffx linear iterations at : 03:41:18 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 2.4747964E-05 3.7441254E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 03:41:19 3.385u 0.168s 0:04.12 85.9% 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 Tue Oct 11 2011 at 03:41:19 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3086 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.972445 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): -11.77000 37.21900 ymin,ymax (A): -27.26200 21.56200 zmin,zma (A): -8.514999 45.63100 x,y,z range (A): 48.98900 48.82400 54.14600 scale (grids/A): 1.972445 object centre (A): 12.72450 -2.849999 18.55800 number of atom coordinates read : 3086 total number of charged atoms : 2682 net assigned charge : -0.8379797 assigned positive charge : 426.3576 centred at (gu) : 90.35909 92.12382 94.10883 assigned negative charge : -427.1962 centred at (gu) : 89.63032 91.89449 93.86409 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 88943 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23885 grid for indexing accessible points = 1.400000 m= 35223 mr = 63579 m= 6549 mr = 26972 m= 447 mr = 4254 m= 7 mr = 159 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 470 time to turn everything in is 0.6200000 number of dielectric boundary points 36205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 21155 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) : 0.6574816 object centre at (A) : 12.72450 -2.849999 18.55800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1476738E-02 -2.0475546E-03 midg,1,midg; midg,igrid,midg -1.2018100E-02 2.9292842E-03 1,midg,midg; igrid,midg,midg -1.2187115E-02 6.5999761E-02 gauss-seidel spectral radius is 0.9987460 estimated iterations to convergence 224 setup time was (sec) 0.9100000 now iterating at: 03:41:20 rms-change max change #iterations 4.800529 218.4939 at 10iterations 2.333431 82.34311 at 20iterations 1.128520 35.96780 at 30iterations 0.5472037 15.96045 at 40iterations 0.2651464 7.643059 at 50iterations 0.1281407 3.984368 at 60iterations 6.2048119E-02 1.726820 at 70iterations 2.9992554E-02 0.8616199 at 80iterations 1.4622140E-02 0.4180855 at 90iterations 7.0820856E-03 0.2049828 at 100iterations 3.4274203E-03 0.1000519 at 110iterations 1.6673270E-03 4.7559738E-02 at 120iterations finished qdiffx linear iterations at : 03:41:27 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 1.6673270E-03 4.7559738E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 03:41:28 7.635u 0.194s 0:08.45 92.5% 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 Tue Oct 11 2011 at 03:41:28 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3086 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.958667 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): -11.77000 37.21900 ymin,ymax (A): -27.26200 21.56200 zmin,zma (A): -8.514999 45.63100 x,y,z range (A): 48.98900 48.82400 54.14600 scale (grids/A): 2.958667 object centre (A): 12.72450 -2.849999 18.55800 number of atom coordinates read : 3086 total number of charged atoms : 2682 net assigned charge : -0.8379797 assigned positive charge : 426.3576 centred at (gu) : 90.53854 93.18573 96.16322 assigned negative charge : -427.1962 centred at (gu) : 89.44534 92.84163 95.79600 start vw surface at 0.1600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 204935 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23885 grid for indexing accessible points = 1.400000 m= 110942 mr = 152937 m= 44563 mr = 92837 m= 12057 mr = 36729 m= 1913 mr = 9151 m= 132 mr = 1293 m= 3 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 1736 time to turn everything in is 1.650000 number of dielectric boundary points 81545 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 21440 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) : 1.972445 object centre at (A) : 12.72450 -2.849999 18.55800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3437101 0.1972558 midg,1,midg; midg,igrid,midg -0.1524169 7.8417897E-02 1,midg,midg; igrid,midg,midg -3.0537322E-02 0.5813276 gauss-seidel spectral radius is 0.9992868 estimated iterations to convergence 295 setup time was (sec) 1.960000 now iterating at: 03:41:30 rms-change max change #iterations 10.95920 484.8441 at 10iterations 6.462288 142.0800 at 20iterations 3.794755 82.88749 at 30iterations 2.225983 41.39431 at 40iterations 1.302834 22.25726 at 50iterations 0.7633360 13.09054 at 60iterations 0.4462414 9.140524 at 70iterations 0.2598726 4.372498 at 80iterations 0.1518647 2.937940 at 90iterations 8.8523366E-02 1.555847 at 100iterations 5.1674709E-02 0.9388428 at 110iterations 3.0062251E-02 0.4950132 at 120iterations 1.7529082E-02 0.3088646 at 130iterations 1.0224943E-02 0.1609354 at 140iterations 5.9672198E-03 9.7313076E-02 at 150iterations 3.4875351E-03 5.9616089E-02 at 160iterations 2.0463774E-03 3.4858704E-02 at 170iterations 1.2105515E-03 2.2068024E-02 at 180iterations finished qdiffx linear iterations at : 03:41:43 total time elapsed so far: 14.95000 # loops : 180 mean,max change (kT/e) : 1.2105515E-03 2.2068024E-02 energy calculations done at 14.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.12000 DelPhi exited at 03:41:43 15.126u 0.267s 0:15.74 97.7% 0+0k 0+0io 0pf+0w