Sat Oct 15 15:20:49 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 Sat Oct 15 2011 at 15:20:49 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2798 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6626585 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): -10.39400 37.75300 ymin,ymax (A): -25.66700 22.94100 zmin,zma (A): -8.587000 45.13600 x,y,z range (A): 48.14700 48.60800 53.72300 scale (grids/A): 0.6626585 object centre (A): 13.67950 -1.363000 18.27450 number of atom coordinates read : 2798 total number of charged atoms : 2646 net assigned charge : 2.140011 assigned positive charge : 423.7836 centred at (gu) : 89.73129 90.49745 91.12378 assigned negative charge : -421.6443 centred at (gu) : 89.48794 90.33960 91.08296 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8297 nv = 96 ne = 84 npr = 56389 no. pairs analyzed = 56389 no. exposed pairs = 3471 no. arc points = 23954 no. surface atoms = 1166 nbur = 1632 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4705 m= 3 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.2100000 number of dielectric boundary points 4004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2326 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9721 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8020166E-09 1.9128521E-08 midg,1,midg; midg,igrid,midg -2.7959480E-08 4.6042999E-08 1,midg,midg; igrid,midg,midg -5.4640275E-08 5.6989663E-08 gauss-seidel spectral radius is 0.9882118 estimated iterations to convergence 75 setup time was (sec) 0.4000000 now iterating at: 15:20:50 rms-change max change #iterations 0.1737905 25.95945 at 10iterations 1.8906133E-02 3.322140 at 20iterations 2.1070309E-03 0.2447701 at 30iterations 2.7634003E-04 3.8337708E-02 at 40iterations 5.2981515E-05 6.2770844E-03 at 50iterations finished qdiffx linear iterations at : 15:20:52 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 5.2981515E-05 6.2770844E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 15:20:53 3.398u 0.164s 0:03.93 90.3% 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 Sat Oct 15 2011 at 15:20:53 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2798 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.987975 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): -10.39400 37.75300 ymin,ymax (A): -25.66700 22.94100 zmin,zma (A): -8.587000 45.13600 x,y,z range (A): 48.14700 48.60800 53.72300 scale (grids/A): 1.987975 object centre (A): 13.67950 -1.363000 18.27450 number of atom coordinates read : 2798 total number of charged atoms : 2646 net assigned charge : 2.140011 assigned positive charge : 423.7836 centred at (gu) : 89.19299 91.49185 93.37054 assigned negative charge : -421.6443 centred at (gu) : 88.46388 91.01832 93.24847 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 89043 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23954 grid for indexing accessible points = 1.400000 m= 33240 mr = 63033 m= 5485 mr = 24883 m= 373 mr = 3379 m= 10 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 757 time to turn everything in is 0.4300000 number of dielectric boundary points 36722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20926 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) : 0.6626585 object centre at (A) : 13.67950 -1.363000 18.27450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3015260E-02 7.9377256E-03 midg,1,midg; midg,igrid,midg -1.8426813E-02 9.5787905E-03 1,midg,midg; igrid,midg,midg -1.9686734E-02 7.5107425E-02 gauss-seidel spectral radius is 0.9987620 estimated iterations to convergence 225 setup time was (sec) 0.6300000 now iterating at: 15:20:54 rms-change max change #iterations 4.854297 223.9621 at 10iterations 2.369142 68.64224 at 20iterations 1.143470 35.06015 at 30iterations 0.5569748 16.19483 at 40iterations 0.2710251 9.046734 at 50iterations 0.1316397 3.796276 at 60iterations 6.3947901E-02 2.035717 at 70iterations 3.1226244E-02 0.9575710 at 80iterations 1.5162834E-02 0.4643545 at 90iterations 7.3739458E-03 0.2026072 at 100iterations 3.5948968E-03 9.4298124E-02 at 110iterations 1.7513346E-03 5.3977966E-02 at 120iterations finished qdiffx linear iterations at : 15:21:01 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.7513346E-03 5.3977966E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 15:21:01 7.879u 0.217s 0:08.43 95.8% 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 Sat Oct 15 2011 at 15:21:02 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2798 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.981963 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): -10.39400 37.75300 ymin,ymax (A): -25.66700 22.94100 zmin,zma (A): -8.587000 45.13600 x,y,z range (A): 48.14700 48.60800 53.72300 scale (grids/A): 2.981963 object centre (A): 13.67950 -1.363000 18.27450 number of atom coordinates read : 2798 total number of charged atoms : 2646 net assigned charge : 2.140011 assigned positive charge : 423.7836 centred at (gu) : 88.78944 92.23762 95.05579 assigned negative charge : -421.6443 centred at (gu) : 87.69572 91.52740 94.87247 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 205393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23954 grid for indexing accessible points = 1.400000 m= 107196 mr = 152101 m= 39834 mr = 88544 m= 9970 mr = 32187 m= 1579 mr = 7339 m= 110 mr = 1055 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 2765 time to turn everything in is 1.140000 number of dielectric boundary points 82810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 21158 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) : 1.987975 object centre at (A) : 13.67950 -1.363000 18.27450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9730901 0.2644473 midg,1,midg; midg,igrid,midg -0.2210021 5.1834248E-02 1,midg,midg; igrid,midg,midg -0.1493052 0.6314269 gauss-seidel spectral radius is 0.9992923 estimated iterations to convergence 297 setup time was (sec) 1.380000 now iterating at: 15:21:03 rms-change max change #iterations 11.13935 430.7472 at 10iterations 6.578366 137.1682 at 20iterations 3.870833 76.84015 at 30iterations 2.278119 43.45169 at 40iterations 1.338996 23.96582 at 50iterations 0.7833118 15.05324 at 60iterations 0.4600756 9.093782 at 70iterations 0.2690646 4.781280 at 80iterations 0.1572181 2.793504 at 90iterations 9.1778763E-02 1.608061 at 100iterations 5.3688679E-02 0.9208260 at 110iterations 3.1332683E-02 0.5231609 at 120iterations 1.8274968E-02 0.2911911 at 130iterations 1.0698715E-02 0.1823196 at 140iterations 6.2561450E-03 0.1049328 at 150iterations 3.6822415E-03 6.2389374E-02 at 160iterations 2.1761314E-03 3.8652897E-02 at 170iterations 1.2997149E-03 2.1403313E-02 at 180iterations finished qdiffx linear iterations at : 15:21:15 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 1.2997149E-03 2.1403313E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 15:21:15 13.007u 0.218s 0:13.65 96.7% 0+0k 0+0io 0pf+0w