Tue Oct 11 08:07:11 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 Tue Oct 11 2011 at 08:07:12 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: 236 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 : 7.000020 assigned positive charge : 401.7335 centred at (gu) : 90.11157 90.60764 91.06700 assigned negative charge : -394.7345 centred at (gu) : 89.93775 90.69352 90.99249 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 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 = 0.1700000 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 1.1820879E-10 5.6129514E-09 midg,1,midg; midg,igrid,midg 4.1050496E-09 -2.6083852E-10 1,midg,midg; igrid,midg,midg -2.7322964E-09 7.3451627E-09 gauss-seidel spectral radius is 0.9852423 estimated iterations to convergence 68 setup time was (sec) 0.6400000 now iterating at: 08:07:12 rms-change max change #iterations 0.1002315 14.76260 at 10iterations 8.0702072E-03 1.192038 at 20iterations 6.5682369E-04 0.1135359 at 30iterations 5.4026383E-05 8.5475445E-03 at 40iterations 4.6146552E-06 6.7138672E-04 at 50iterations finished qdiffx linear iterations at : 08:07:16 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 4.6146552E-06 6.7138672E-04 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 08:07:16 4.156u 0.281s 0:04.94 89.6% 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 08:07:16 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: 236 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 : 7.000020 assigned positive charge : 401.7335 centred at (gu) : 90.33408 91.82238 93.20032 assigned negative charge : -394.7345 centred at (gu) : 89.81301 92.08036 92.97727 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 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 0.6200000 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 3.9365208E-03 3.7990473E-02 midg,1,midg; midg,igrid,midg 1.1185403E-02 4.6188133E-03 1,midg,midg; igrid,midg,midg -2.4631780E-02 1.2028461E-02 gauss-seidel spectral radius is 0.9984499 estimated iterations to convergence 201 setup time was (sec) 0.9300000 now iterating at: 08:07:18 rms-change max change #iterations 3.709698 155.9734 at 10iterations 1.650576 60.46126 at 20iterations 0.7314088 30.11158 at 30iterations 0.3252852 11.29920 at 40iterations 0.1445255 4.644493 at 50iterations 6.4309567E-02 2.318248 at 60iterations 2.8692909E-02 0.9908028 at 70iterations 1.2711506E-02 0.4890938 at 80iterations 5.6528328E-03 0.1995327 at 90iterations 2.5241449E-03 8.8045120E-02 at 100iterations 1.1235713E-03 4.1152954E-02 at 110iterations 5.0051173E-04 1.7569542E-02 at 120iterations finished qdiffx linear iterations at : 08:07:26 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 5.0051173E-04 1.7569542E-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 08:07:27 9.573u 0.311s 0:10.46 94.4% 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 08:07:27 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: 236 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 : 7.000020 assigned positive charge : 401.7335 centred at (gu) : 90.50098 92.73331 94.80017 assigned negative charge : -394.7345 centred at (gu) : 89.71947 93.12048 94.46588 start vw surface at 0.1500000 fill in re-entrant regions at 0.5200000 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 1.520000 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 1.680000 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 -2.8732542E-02 0.4002326 midg,1,midg; midg,igrid,midg 5.4607771E-02 0.2165756 1,midg,midg; igrid,midg,midg -0.3390543 0.1903114 gauss-seidel spectral radius is 0.9992164 estimated iterations to convergence 282 setup time was (sec) 1.860000 now iterating at: 08:07:29 rms-change max change #iterations 9.134958 298.4103 at 10iterations 5.275293 132.1856 at 20iterations 3.020331 61.97464 at 30iterations 1.721697 36.31956 at 40iterations 0.9773110 22.03060 at 50iterations 0.5550299 11.89343 at 60iterations 0.3143828 6.850755 at 70iterations 0.1779614 3.465910 at 80iterations 0.1004381 1.932784 at 90iterations 5.6984823E-02 1.330060 at 100iterations 3.2181993E-02 0.7094841 at 110iterations 1.8170297E-02 0.3444595 at 120iterations 1.0256342E-02 0.1923280 at 130iterations 5.8022039E-03 0.1102219 at 140iterations 3.2729683E-03 7.1376801E-02 at 150iterations 1.8482727E-03 3.4332275E-02 at 160iterations 1.0449728E-03 2.1696568E-02 at 170iterations 5.8848917E-04 1.0838509E-02 at 180iterations finished qdiffx linear iterations at : 08:07:43 total time elapsed so far: 15.78000 # loops : 180 mean,max change (kT/e) : 5.8848917E-04 1.0838509E-02 energy calculations done at 15.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.96000 DelPhi exited at 08:07:44 15.963u 0.335s 0:16.70 97.5% 0+0k 0+0io 0pf+0w