Mon Oct 10 17:14:56 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 Mon Oct 10 2011 at 17:14:56 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 !!! WARNING: HIR 119 has a net charge of 0.5140 !!! WARNING: HIR 123 has a net charge of 0.5140 !!! WARNING: HIR 129 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6660430 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): 42.11900 84.89100 ymin,ymax (A): 64.59400 111.5340 zmin,zma (A): 24.26200 77.71200 x,y,z range (A): 42.77200 46.94000 53.45000 scale (grids/A): 0.6660430 object centre (A): 63.50500 88.06400 50.98700 number of atom coordinates read : 2010 total number of charged atoms : 1881 net assigned charge : -7.457989 assigned positive charge : 290.4969 centred at (gu) : 89.70887 90.30050 89.43380 assigned negative charge : -297.9550 centred at (gu) : 89.78435 90.14395 89.56610 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6213 nv = 96 ne = 84 npr = 41289 no. pairs analyzed = 41289 no. exposed pairs = 2706 no. arc points = 20384 no. surface atoms = 904 nbur = 1106 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 352 mr = 3177 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.1700000 number of dielectric boundary points 3364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1814 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7046 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2395335E-10 -4.1239709E-08 midg,1,midg; midg,igrid,midg -4.7693785E-08 5.1442428E-09 1,midg,midg; igrid,midg,midg -9.7717532E-09 -3.3942818E-08 gauss-seidel spectral radius is 0.9882729 estimated iterations to convergence 75 setup time was (sec) 0.3600000 now iterating at: 17:14:56 rms-change max change #iterations 0.1617008 24.99590 at 10iterations 1.7416267E-02 2.801960 at 20iterations 1.9187393E-03 0.2682571 at 30iterations 2.2200801E-04 3.3512115E-02 at 40iterations 2.8012499E-05 3.7231445E-03 at 50iterations finished qdiffx linear iterations at : 17:14:59 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 2.8012499E-05 3.7231445E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 17:14:59 3.324u 0.142s 0:03.74 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 Mon Oct 10 2011 at 17:14:59 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 !!! WARNING: HIR 119 has a net charge of 0.5140 !!! WARNING: HIR 123 has a net charge of 0.5140 !!! WARNING: HIR 129 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.998129 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): 42.11900 84.89100 ymin,ymax (A): 64.59400 111.5340 zmin,zma (A): 24.26200 77.71200 x,y,z range (A): 42.77200 46.94000 53.45000 scale (grids/A): 1.998129 object centre (A): 63.50500 88.06400 50.98700 number of atom coordinates read : 2010 total number of charged atoms : 1881 net assigned charge : -7.457989 assigned positive charge : 290.4969 centred at (gu) : 89.12652 90.90141 88.30149 assigned negative charge : -297.9550 centred at (gu) : 89.35286 90.43182 88.69820 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66063 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20384 grid for indexing accessible points = 1.400000 m= 22743 mr = 43408 m= 3592 mr = 16136 m= 204 mr = 1993 m= 5 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1568 time to turn everything in is 0.3200000 number of dielectric boundary points 30990 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 14890 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) : 0.6660430 object centre at (A) : 63.50500 88.06400 50.98700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4246780E-02 -6.2777184E-02 midg,1,midg; midg,igrid,midg -2.6201475E-02 2.4936920E-02 1,midg,midg; igrid,midg,midg -1.6340168E-02 -2.0203723E-02 gauss-seidel spectral radius is 0.9987139 estimated iterations to convergence 221 setup time was (sec) 0.5300000 now iterating at: 17:15:00 rms-change max change #iterations 4.067896 193.1508 at 10iterations 1.933262 71.00009 at 20iterations 0.9272962 30.40088 at 30iterations 0.4432787 15.72000 at 40iterations 0.2113695 7.229985 at 50iterations 0.1014563 3.348852 at 60iterations 4.8219364E-02 1.718986 at 70iterations 2.3215730E-02 0.7931366 at 80iterations 1.1074733E-02 0.3681955 at 90iterations 5.2831131E-03 0.1878548 at 100iterations 2.5381877E-03 9.7488403E-02 at 110iterations 1.2206214E-03 4.8791885E-02 at 120iterations finished qdiffx linear iterations at : 17:15:07 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 1.2206214E-03 4.8791885E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 17:15:08 7.605u 0.197s 0:08.11 96.0% 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 Mon Oct 10 2011 at 17:15:08 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 !!! WARNING: HIR 119 has a net charge of 0.5140 !!! WARNING: HIR 123 has a net charge of 0.5140 !!! WARNING: HIR 129 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.997194 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): 42.11900 84.89100 ymin,ymax (A): 64.59400 111.5340 zmin,zma (A): 24.26200 77.71200 x,y,z range (A): 42.77200 46.94000 53.45000 scale (grids/A): 2.997194 object centre (A): 63.50500 88.06400 50.98700 number of atom coordinates read : 2010 total number of charged atoms : 1881 net assigned charge : -7.457989 assigned positive charge : 290.4969 centred at (gu) : 88.68972 91.35222 87.45210 assigned negative charge : -297.9550 centred at (gu) : 89.02925 90.64764 88.04729 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 152434 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20384 grid for indexing accessible points = 1.400000 m= 73398 mr = 105475 m= 26112 mr = 58464 m= 6265 mr = 20440 m= 958 mr = 4416 m= 75 mr = 582 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 5302 time to turn everything in is 0.8200000 number of dielectric boundary points 69839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 15048 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) : 1.998129 object centre at (A) : 63.50500 88.06400 50.98700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8633938 -0.6691768 midg,1,midg; midg,igrid,midg -0.2327368 0.2483916 1,midg,midg; igrid,midg,midg -0.1925119 -0.1843880 gauss-seidel spectral radius is 0.9992791 estimated iterations to convergence 294 setup time was (sec) 1.050000 now iterating at: 17:15:09 rms-change max change #iterations 9.377741 526.9213 at 10iterations 5.497990 127.6168 at 20iterations 3.222199 78.93021 at 30iterations 1.883303 38.56160 at 40iterations 1.095440 24.03340 at 50iterations 0.6377524 13.34326 at 60iterations 0.3710974 6.993289 at 70iterations 0.2155199 4.729476 at 80iterations 0.1251504 2.788488 at 90iterations 7.2637893E-02 1.452927 at 100iterations 4.2076189E-02 0.7749786 at 110iterations 2.4396384E-02 0.4744873 at 120iterations 1.4172703E-02 0.2855062 at 130iterations 8.2223788E-03 0.1557198 at 140iterations 4.7523300E-03 9.4608963E-02 at 150iterations 2.7526701E-03 5.3238392E-02 at 160iterations 1.6014607E-03 3.5095215E-02 at 170iterations 9.2988921E-04 1.8378258E-02 at 180iterations finished qdiffx linear iterations at : 17:15:20 total time elapsed so far: 12.12000 # loops : 180 mean,max change (kT/e) : 9.2988921E-04 1.8378258E-02 energy calculations done at 12.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 17:15:20 12.258u 0.204s 0:12.79 97.3% 0+0k 0+0io 0pf+0w