Sat Oct 15 13:56:00 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 Sat Oct 15 2011 at 13:56:00 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2620 !!! WARNING: HIR 119 has a net charge of 0.5140 !!! WARNING: ASP 501 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5285506 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): -16.49500 46.90400 ymin,ymax (A): -3.971000 45.54500 zmin,zma (A): -27.25700 40.09700 x,y,z range (A): 63.39900 49.51600 67.35400 scale (grids/A): 0.5285506 object centre (A): 15.20450 20.78700 6.420000 number of atom coordinates read : 2620 total number of charged atoms : 2489 net assigned charge : -4.985981 assigned positive charge : 383.2931 centred at (gu) : 90.07597 91.74108 92.14394 assigned negative charge : -388.2793 centred at (gu) : 90.23537 91.79779 92.05533 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4866 nv = 96 ne = 84 npr = 51629 no. pairs analyzed = 51629 no. exposed pairs = 3686 no. arc points = 27465 no. surface atoms = 1233 nbur = 1387 mkacc time = 9.0000004E-02 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= 151 mr = 2153 m= 0 mr = 3 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2664 ## 382 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6375 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4290431E-10 1.8716176E-10 midg,1,midg; midg,igrid,midg 5.0679981E-12 -5.0252852E-10 1,midg,midg; igrid,midg,midg 2.9764191E-10 -6.4351430E-10 gauss-seidel spectral radius is 0.9815461 estimated iterations to convergence 61 setup time was (sec) 0.3900000 now iterating at: 13:56:01 rms-change max change #iterations 6.4170241E-02 13.18118 at 10iterations 3.8162782E-03 0.6553602 at 20iterations 2.2992821E-04 4.1599274E-02 at 30iterations 1.3613889E-05 2.5138855E-03 at 40iterations 8.9108255E-07 2.0408630E-04 at 50iterations finished qdiffx linear iterations at : 13:56:04 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 8.9108255E-07 2.0408630E-04 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 13:56:04 3.619u 0.215s 0:04.24 90.0% 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 13:56:04 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2620 !!! WARNING: HIR 119 has a net charge of 0.5140 !!! WARNING: ASP 501 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.585652 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): -16.49500 46.90400 ymin,ymax (A): -3.971000 45.54500 zmin,zma (A): -27.25700 40.09700 x,y,z range (A): 63.39900 49.51600 67.35400 scale (grids/A): 1.585652 object centre (A): 15.20450 20.78700 6.420000 number of atom coordinates read : 2620 total number of charged atoms : 2489 net assigned charge : -4.985981 assigned positive charge : 383.2931 centred at (gu) : 90.22764 95.22271 96.43144 assigned negative charge : -388.2793 centred at (gu) : 90.70606 95.39324 96.16562 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 53732 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27465 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 13435 mr = 33114 m= 1021 mr = 8137 m= 18 mr = 376 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 1225 time to turn everything in is 0.2800000 number of dielectric boundary points 26578 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 317 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 18969 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) : 0.5285506 object centre at (A) : 15.20450 20.78700 6.420000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2486909E-02 4.5394986E-03 midg,1,midg; midg,igrid,midg -7.6947012E-04 -8.6399280E-03 1,midg,midg; igrid,midg,midg 1.2986957E-02 -1.3401818E-02 gauss-seidel spectral radius is 0.9980451 estimated iterations to convergence 180 setup time was (sec) 0.5000000 now iterating at: 13:56:05 rms-change max change #iterations 2.899015 148.2126 at 10iterations 1.162984 54.59692 at 20iterations 0.4656624 21.81951 at 30iterations 0.1868562 7.986325 at 40iterations 7.5318143E-02 3.527200 at 50iterations 3.0089481E-02 1.178696 at 60iterations 1.2153618E-02 0.5421143 at 70iterations 4.9000210E-03 0.2186332 at 80iterations 1.9741117E-03 8.3447933E-02 at 90iterations 7.9461734E-04 3.6714792E-02 at 100iterations 3.1954577E-04 1.3534546E-02 at 110iterations 1.2880997E-04 5.2986145E-03 at 120iterations finished qdiffx linear iterations at : 13:56:12 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 1.2880997E-04 5.2986145E-03 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 13:56:13 8.137u 0.251s 0:08.65 96.8% 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 13:56:13 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2620 !!! WARNING: HIR 119 has a net charge of 0.5140 !!! WARNING: ASP 501 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.378478 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): -16.49500 46.90400 ymin,ymax (A): -3.971000 45.54500 zmin,zma (A): -27.25700 40.09700 x,y,z range (A): 63.39900 49.51600 67.35400 scale (grids/A): 2.378478 object centre (A): 15.20450 20.78700 6.420000 number of atom coordinates read : 2620 total number of charged atoms : 2489 net assigned charge : -4.985981 assigned positive charge : 383.2931 centred at (gu) : 90.34128 97.83398 99.64696 assigned negative charge : -388.2793 centred at (gu) : 91.05896 98.08976 99.24845 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 125282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27465 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 48995 mr = 82426 m= 10986 mr = 36132 m= 1453 mr = 7359 m= 74 mr = 833 m= 0 mr = 40 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 4102 time to turn everything in is 0.6500000 number of dielectric boundary points 60000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 19869 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) : 1.585652 object centre at (A) : 15.20450 20.78700 6.420000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4572660 -2.2897540E-02 midg,1,midg; midg,igrid,midg -2.8496310E-03 -0.1251711 1,midg,midg; igrid,midg,midg 0.1605387 -0.2445194 gauss-seidel spectral radius is 0.9990891 estimated iterations to convergence 262 setup time was (sec) 0.8900000 now iterating at: 13:56:15 rms-change max change #iterations 7.672615 256.9834 at 10iterations 4.242175 127.6197 at 20iterations 2.333062 62.66722 at 30iterations 1.270804 34.12457 at 40iterations 0.6931317 17.60715 at 50iterations 0.3762674 8.945332 at 60iterations 0.2037898 5.292178 at 70iterations 0.1103597 2.683559 at 80iterations 5.9543490E-02 1.390656 at 90iterations 3.2109533E-02 0.7425632 at 100iterations 1.7423932E-02 0.3969345 at 110iterations 9.4004450E-03 0.2468886 at 120iterations 5.0610318E-03 0.1070404 at 130iterations 2.7341626E-03 5.9844971E-02 at 140iterations 1.4722499E-03 3.5530090E-02 at 150iterations 7.9182797E-04 1.6410828E-02 at 160iterations 4.2873106E-04 9.5558167E-03 at 170iterations 2.3113830E-04 4.8484802E-03 at 180iterations finished qdiffx linear iterations at : 13:56:38 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 2.3113830E-04 4.8484802E-03 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 13:56:39 12.482u 0.223s 0:25.68 49.4% 0+0k 0+0io 0pf+0w