Tue Oct 11 08:07:44 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 Tue Oct 11 2011 at 08:07:44 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2714 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5918045 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): -18.53900 38.29600 ymin,ymax (A): -32.23000 27.92500 zmin,zma (A): -22.61800 36.32800 x,y,z range (A): 56.83500 60.15500 58.94600 scale (grids/A): 0.5918045 object centre (A): 9.878499 -2.152500 6.855001 number of atom coordinates read : 2714 total number of charged atoms : 2571 net assigned charge : 7.000018 assigned positive charge : 404.5335 centred at (gu) : 90.14216 90.57241 91.07038 assigned negative charge : -397.5345 centred at (gu) : 89.97189 90.66161 90.99354 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6304 nv = 96 ne = 84 npr = 54104 no. pairs analyzed = 54104 no. exposed pairs = 3548 no. arc points = 25114 no. surface atoms = 1198 nbur = 1516 mkacc time = 0.1500000 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 = 1.456000 m= 258 mr = 3179 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3600000 number of dielectric boundary points 3365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2526 ## 278 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7894 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0551670E-11 5.7184226E-09 midg,1,midg; midg,igrid,midg 4.2327151E-09 -3.9282441E-10 1,midg,midg; igrid,midg,midg -2.6466205E-09 7.3284165E-09 gauss-seidel spectral radius is 0.9852423 estimated iterations to convergence 68 setup time was (sec) 0.6400000 now iterating at: 08:07:45 rms-change max change #iterations 0.1024413 14.74593 at 10iterations 8.2550263E-03 1.283314 at 20iterations 6.6985079E-04 0.1091862 at 30iterations 5.5373395E-05 8.8946819E-03 at 40iterations 4.7057570E-06 6.7901611E-04 at 50iterations finished qdiffx linear iterations at : 08:07:48 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 4.7057570E-06 6.7901611E-04 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 08:07:49 4.155u 0.270s 0:04.85 91.1% 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 Tue Oct 11 2011 at 08:07:49 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2714 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.775414 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): -18.53900 38.29600 ymin,ymax (A): -32.23000 27.92500 zmin,zma (A): -22.61800 36.32800 x,y,z range (A): 56.83500 60.15500 58.94600 scale (grids/A): 1.775414 object centre (A): 9.878499 -2.152500 6.855001 number of atom coordinates read : 2714 total number of charged atoms : 2571 net assigned charge : 7.000018 assigned positive charge : 404.5335 centred at (gu) : 90.42585 91.71675 93.21051 assigned negative charge : -397.5345 centred at (gu) : 89.91542 91.98458 92.98033 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 69090 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25114 grid for indexing accessible points = 1.400000 m= 21376 mr = 46011 m= 2513 mr = 14708 m= 110 mr = 1249 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 541 time to turn everything in is 0.6100000 number of dielectric boundary points 31105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20018 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) : 0.5918045 object centre at (A) : 9.878499 -2.152500 6.855001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5213719E-03 3.8218774E-02 midg,1,midg; midg,igrid,midg 1.2176717E-02 4.5127100E-03 1,midg,midg; igrid,midg,midg -2.4480186E-02 1.1937589E-02 gauss-seidel spectral radius is 0.9984499 estimated iterations to convergence 201 setup time was (sec) 0.9100000 now iterating at: 08:07:50 rms-change max change #iterations 3.746144 155.9734 at 10iterations 1.667637 60.46125 at 20iterations 0.7385565 30.11159 at 30iterations 0.3283939 11.37732 at 40iterations 0.1459541 4.633387 at 50iterations 6.4926021E-02 2.315569 at 60iterations 2.8969465E-02 1.010197 at 70iterations 1.2831107E-02 0.4858170 at 80iterations 5.7057566E-03 0.2036812 at 90iterations 2.5480252E-03 8.7066650E-02 at 100iterations 1.1344751E-03 4.2388916E-02 at 110iterations 5.0530909E-04 1.7488480E-02 at 120iterations finished qdiffx linear iterations at : 08:07:58 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 5.0530909E-04 1.7488480E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.570000 DelPhi exited at 08:07:59 9.572u 0.316s 0:10.30 95.9% 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 Tue Oct 11 2011 at 08:07:59 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2714 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.663120 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): -18.53900 38.29600 ymin,ymax (A): -32.23000 27.92500 zmin,zma (A): -22.61800 36.32800 x,y,z range (A): 56.83500 60.15500 58.94600 scale (grids/A): 2.663120 object centre (A): 9.878499 -2.152500 6.855001 number of atom coordinates read : 2714 total number of charged atoms : 2571 net assigned charge : 7.000018 assigned positive charge : 404.5335 centred at (gu) : 90.63864 92.57488 94.81544 assigned negative charge : -397.5345 centred at (gu) : 89.87305 92.97679 94.47046 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 160419 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25114 grid for indexing accessible points = 1.400000 m= 73106 mr = 112854 m= 21724 mr = 57546 m= 4050 mr = 16361 m= 445 mr = 2652 m= 11 mr = 230 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 1692 time to turn everything in is 1.540000 number of dielectric boundary points 70112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 20559 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) : 1.775414 object centre at (A) : 9.878499 -2.152500 6.855001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3795204E-02 0.4028619 midg,1,midg; midg,igrid,midg 6.7888886E-02 0.2156196 1,midg,midg; igrid,midg,midg -0.3373951 0.1896666 gauss-seidel spectral radius is 0.9992164 estimated iterations to convergence 282 setup time was (sec) 1.870000 now iterating at: 08:08:01 rms-change max change #iterations 9.212159 298.4103 at 10iterations 5.316240 132.1785 at 20iterations 3.044218 62.02679 at 30iterations 1.734438 37.51373 at 40iterations 0.9845597 21.71658 at 50iterations 0.5590219 11.96662 at 60iterations 0.3166883 6.881696 at 70iterations 0.1791749 3.524914 at 80iterations 0.1011240 1.924111 at 90iterations 5.7368234E-02 1.313202 at 100iterations 3.2399472E-02 0.7089319 at 110iterations 1.8293768E-02 0.3424501 at 120iterations 1.0323187E-02 0.1918297 at 130iterations 5.8408473E-03 0.1114044 at 140iterations 3.2949620E-03 7.1876526E-02 at 150iterations 1.8602088E-03 3.4492493E-02 at 160iterations 1.0517621E-03 2.1658421E-02 at 170iterations 5.9225579E-04 1.0976553E-02 at 180iterations finished qdiffx linear iterations at : 08:08:15 total time elapsed so far: 15.79000 # loops : 180 mean,max change (kT/e) : 5.9225579E-04 1.0976553E-02 energy calculations done at 15.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.98000 DelPhi exited at 08:08:16 15.979u 0.305s 0:16.64 97.7% 0+0k 0+0io 0pf+0w