Sat Oct 15 11:29:06 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 11:29:06 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 423 has a net charge of 1.4000 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: 0.6215734 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): -31.30800 17.52900 ymin,ymax (A): -24.03000 22.12900 zmin,zma (A): -12.37100 44.90300 x,y,z range (A): 48.83700 46.15900 57.27400 scale (grids/A): 0.6215734 object centre (A): -6.889501 -0.9504995 16.26600 number of atom coordinates read : 2591 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.47772 89.58677 89.64065 assigned negative charge : -387.4045 centred at (gu) : 88.37549 89.63799 89.52923 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6632 nv = 96 ne = 84 npr = 53486 no. pairs analyzed = 53486 no. exposed pairs = 3048 no. arc points = 21707 no. surface atoms = 1019 nbur = 1572 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3731 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 0.3200000 number of dielectric boundary points 3205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2113 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8123 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6740678E-09 1.0288485E-08 midg,1,midg; midg,igrid,midg 7.7077997E-09 -3.2000909E-11 1,midg,midg; igrid,midg,midg -5.2327636E-09 7.5425284E-09 gauss-seidel spectral radius is 0.9865929 estimated iterations to convergence 71 setup time was (sec) 0.7200000 now iterating at: 11:29:07 rms-change max change #iterations 0.1313327 22.40712 at 10iterations 1.1990504E-02 1.814512 at 20iterations 1.1166756E-03 0.1590538 at 30iterations 1.0438415E-04 1.5157700E-02 at 40iterations 1.0034520E-05 1.5125275E-03 at 50iterations finished qdiffx linear iterations at : 11:29:12 total time elapsed so far: 5.200000 # loops : 50 mean,max change (kT/e) : 1.0034520E-05 1.5125275E-03 energy calculations done at 5.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.380000 DelPhi exited at 11:29:13 5.381u 0.443s 0:06.52 89.2% 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 Sat Oct 15 2011 at 11:29:13 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 423 has a net charge of 1.4000 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: 1.864720 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): -31.30800 17.52900 ymin,ymax (A): -24.03000 22.12900 zmin,zma (A): -12.37100 44.90300 x,y,z range (A): 48.83700 46.15900 57.27400 scale (grids/A): 1.864720 object centre (A): -6.889501 -0.9504995 16.26600 number of atom coordinates read : 2591 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.43274 88.75980 88.92159 assigned negative charge : -387.4045 centred at (gu) : 85.12625 88.91385 88.58761 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72044 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21707 grid for indexing accessible points = 1.400000 m= 25275 mr = 50436 m= 3544 mr = 18832 m= 160 mr = 2125 m= 4 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 4163 time to turn everything in is 0.6100000 number of dielectric boundary points 29590 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 19275 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) : 0.6215734 object centre at (A) : -6.889501 -0.9504995 16.26600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2113157E-02 1.9814026E-02 midg,1,midg; midg,igrid,midg 1.3836061E-02 2.4392897E-04 1,midg,midg; igrid,midg,midg -4.1149454E-03 3.8957015E-02 gauss-seidel spectral radius is 0.9985765 estimated iterations to convergence 210 setup time was (sec) 0.9600000 now iterating at: 11:29:14 rms-change max change #iterations 4.038742 183.2236 at 10iterations 1.861185 62.30014 at 20iterations 0.8556578 28.78633 at 30iterations 0.3945469 15.52193 at 40iterations 0.1819096 5.666542 at 50iterations 8.3895952E-02 2.811464 at 60iterations 3.8802952E-02 1.203862 at 70iterations 1.7901206E-02 0.5964451 at 80iterations 8.2496069E-03 0.2719975 at 90iterations 3.8077135E-03 0.1207428 at 100iterations 1.7535926E-03 5.5058479E-02 at 110iterations 8.0915145E-04 2.5445938E-02 at 120iterations finished qdiffx linear iterations at : 11:29:26 total time elapsed so far: 12.29000 # loops : 120 mean,max change (kT/e) : 8.0915145E-04 2.5445938E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 11:29:26 12.479u 0.508s 0:13.27 97.7% 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 Sat Oct 15 2011 at 11:29:26 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 423 has a net charge of 1.4000 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: 2.797081 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): -31.30800 17.52900 ymin,ymax (A): -24.03000 22.12900 zmin,zma (A): -12.37100 44.90300 x,y,z range (A): 48.83700 46.15900 57.27400 scale (grids/A): 2.797081 object centre (A): -6.889501 -0.9504995 16.26600 number of atom coordinates read : 2591 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 83.14902 88.13963 88.38228 assigned negative charge : -387.4045 centred at (gu) : 82.68933 88.37056 87.88139 start vw surface at 0.1200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 166845 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21707 grid for indexing accessible points = 1.400000 m= 83317 mr = 122057 m= 28615 mr = 68853 m= 6197 mr = 22970 m= 728 mr = 4548 m= 39 mr = 464 m= 0 mr = 11 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 14680 time to turn everything in is 1.790000 number of dielectric boundary points 66838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 19632 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) : 1.864720 object centre at (A) : -6.889501 -0.9504995 16.26600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1260311 0.2152437 midg,1,midg; midg,igrid,midg 0.1577006 -3.8837690E-02 1,midg,midg; igrid,midg,midg -4.2131405E-02 0.5373595 gauss-seidel spectral radius is 0.9992374 estimated iterations to convergence 286 setup time was (sec) 2.190000 now iterating at: 11:29:29 rms-change max change #iterations 9.465680 335.3411 at 10iterations 5.437296 109.2297 at 20iterations 3.107988 69.30950 at 30iterations 1.774654 32.61721 at 40iterations 1.011550 19.91552 at 50iterations 0.5764841 10.67781 at 60iterations 0.3290126 6.406429 at 70iterations 0.1873525 3.380763 at 80iterations 0.1066923 2.171219 at 90iterations 6.0622275E-02 1.172241 at 100iterations 3.4567386E-02 0.6537824 at 110iterations 1.9682193E-02 0.3675232 at 120iterations 1.1217007E-02 0.2144272 at 130iterations 6.3797450E-03 0.1257019 at 140iterations 3.6359332E-03 6.2532425E-02 at 150iterations 2.0682043E-03 4.1428566E-02 at 160iterations 1.1798702E-03 2.1257401E-02 at 170iterations 6.7352038E-04 1.2170792E-02 at 180iterations finished qdiffx linear iterations at : 11:29:48 total time elapsed so far: 21.33000 # loops : 180 mean,max change (kT/e) : 6.7352038E-04 1.2170792E-02 energy calculations done at 21.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.50000 DelPhi exited at 11:29:48 21.508u 0.529s 0:22.41 98.2% 0+0k 0+0io 0pf+0w