Wed Dec 28 11:02:07 PST 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 Wed Dec 28 2011 at 11:02:08 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6497654 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): -5.057000 35.66000 ymin,ymax (A): -3.927000 48.60200 zmin,zma (A): -24.26700 30.52200 x,y,z range (A): 40.71700 52.52900 54.78900 scale (grids/A): 0.6497654 object centre (A): 15.30150 22.33750 3.127501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 90.36347 92.75800 90.28522 assigned negative charge : -285.8263 centred at (gu) : 90.49940 92.89717 90.19236 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5726 nv = 96 ne = 84 npr = 40444 no. pairs analyzed = 40444 no. exposed pairs = 2377 no. arc points = 17273 no. surface atoms = 808 nbur = 1156 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 3233 m= 0 mr = 43 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.2900000 number of dielectric boundary points 2763 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1679 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6613 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6587384E-09 1.5410926E-08 midg,1,midg; midg,igrid,midg 1.0946868E-08 -2.0887720E-08 1,midg,midg; igrid,midg,midg 1.7728183E-08 -1.1818863E-08 gauss-seidel spectral radius is 0.9876711 estimated iterations to convergence 74 setup time was (sec) 0.5600000 now iterating at: 11:02:09 rms-change max change #iterations 0.1312556 20.69109 at 10iterations 1.3517635E-02 2.311470 at 20iterations 1.3877559E-03 0.2464008 at 30iterations 1.4102273E-04 2.1845818E-02 at 40iterations 1.4688982E-05 2.2454262E-03 at 50iterations finished qdiffx linear iterations at : 11:02:12 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 1.4688982E-05 2.2454262E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 11:02:13 4.481u 0.394s 0:05.31 91.7% 0+0k 0+0io 6pf+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 Wed Dec 28 2011 at 11:02:13 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.949296 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): -5.057000 35.66000 ymin,ymax (A): -3.927000 48.60200 zmin,zma (A): -24.26700 30.52200 x,y,z range (A): 40.71700 52.52900 54.78900 scale (grids/A): 1.949296 object centre (A): 15.30150 22.33750 3.127501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 91.09072 98.27415 90.85558 assigned negative charge : -285.8263 centred at (gu) : 91.49857 98.69171 90.57722 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 60789 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17273 grid for indexing accessible points = 1.400000 m= 23502 mr = 42071 m= 3854 mr = 18244 m= 224 mr = 2565 m= 4 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1479 time to turn everything in is 0.5100000 number of dielectric boundary points 25389 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 14470 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) : 0.6497654 object centre at (A) : 15.30150 22.33750 3.127501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2439729E-02 1.3024189E-02 midg,1,midg; midg,igrid,midg 3.3114027E-02 -1.5721170E-02 1,midg,midg; igrid,midg,midg 7.2182179E-03 -6.8895081E-03 gauss-seidel spectral radius is 0.9986185 estimated iterations to convergence 213 setup time was (sec) 0.8600000 now iterating at: 11:02:14 rms-change max change #iterations 3.720929 157.2418 at 10iterations 1.732643 73.21634 at 20iterations 0.8082941 29.26975 at 30iterations 0.3781308 14.02678 at 40iterations 0.1757959 5.882316 at 50iterations 8.2072310E-02 3.050909 at 60iterations 3.8241066E-02 1.253817 at 70iterations 1.7779913E-02 0.6121950 at 80iterations 8.2780840E-03 0.2686496 at 90iterations 3.8543409E-03 0.1456909 at 100iterations 1.7911886E-03 7.2937012E-02 at 110iterations 8.4024825E-04 3.2650471E-02 at 120iterations finished qdiffx linear iterations at : 11:02:24 total time elapsed so far: 10.23000 # loops : 120 mean,max change (kT/e) : 8.4024825E-04 3.2650471E-02 energy calculations done at 10.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.41000 DelPhi exited at 11:02:25 10.413u 0.469s 0:12.39 87.7% 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 Wed Dec 28 2011 at 11:02:25 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.923944 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): -5.057000 35.66000 ymin,ymax (A): -3.927000 48.60200 zmin,zma (A): -24.26700 30.52200 x,y,z range (A): 40.71700 52.52900 54.78900 scale (grids/A): 2.923944 object centre (A): 15.30150 22.33750 3.127501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 91.63615 102.4112 91.28345 assigned negative charge : -285.8263 centred at (gu) : 92.24774 103.0375 90.86576 start vw surface at 0.1000000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 140089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17273 grid for indexing accessible points = 1.400000 m= 73966 mr = 101354 m= 29340 mr = 62032 m= 7040 mr = 24709 m= 993 mr = 5465 m= 68 mr = 692 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 4790 time to turn everything in is 1.380000 number of dielectric boundary points 57215 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 14656 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) : 1.949296 object centre at (A) : 15.30150 22.33750 3.127501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.059967 3.9888833E-02 midg,1,midg; midg,igrid,midg 0.3087077 -0.1949281 1,midg,midg; igrid,midg,midg 3.8485058E-02 -4.2488087E-02 gauss-seidel spectral radius is 0.9992402 estimated iterations to convergence 286 setup time was (sec) 1.700000 now iterating at: 11:02:28 rms-change max change #iterations 8.709231 478.6741 at 10iterations 4.990722 139.6823 at 20iterations 2.854181 69.91545 at 30iterations 1.623646 34.44972 at 40iterations 0.9298272 19.34322 at 50iterations 0.5291223 10.63080 at 60iterations 0.3018239 5.950904 at 70iterations 0.1715752 3.316454 at 80iterations 9.7569317E-02 1.879445 at 90iterations 5.5485904E-02 1.157162 at 100iterations 3.1611666E-02 0.6760452 at 110iterations 1.8006232E-02 0.3815308 at 120iterations 1.0245462E-02 0.2095947 at 130iterations 5.8255913E-03 0.1179504 at 140iterations 3.3315790E-03 6.0018539E-02 at 150iterations 1.8919039E-03 3.5633087E-02 at 160iterations 1.0748375E-03 2.0431519E-02 at 170iterations 6.1086559E-04 1.1536598E-02 at 180iterations finished qdiffx linear iterations at : 11:02:43 total time elapsed so far: 16.85000 # loops : 180 mean,max change (kT/e) : 6.1086559E-04 1.1536598E-02 energy calculations done at 16.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.02000 DelPhi exited at 11:02:44 17.026u 0.502s 0:19.01 92.1% 0+0k 0+0io 0pf+0w