Mon Oct 10 14:08:59 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 14:08:59 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4471 !!! WARNING: HIQ 440 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5769200 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): -25.56000 35.10500 ymin,ymax (A): 37.76000 99.46700 zmin,zma (A): 30.54600 89.67400 x,y,z range (A): 60.66500 61.70700 59.12800 scale (grids/A): 0.5769200 object centre (A): 4.772500 68.61350 60.11000 number of atom coordinates read : 4471 total number of charged atoms : 4317 net assigned charge : -2.985957 assigned positive charge : 674.3522 centred at (gu) : 90.20128 87.72770 88.58543 assigned negative charge : -677.3412 centred at (gu) : 90.11945 87.81376 88.68143 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9521 nv = 96 ne = 84 npr = 94436 no. pairs analyzed = 94436 no. exposed pairs = 4943 no. arc points = 33445 no. surface atoms = 1684 nbur = 2787 mkacc time = 0.3000000 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 = 1.484000 m= 419 mr = 5598 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.6200000 number of dielectric boundary points 4303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3549 ## 401 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 12535 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0474372E-09 -2.5878168E-09 midg,1,midg; midg,igrid,midg 3.2633212E-09 -1.9416317E-09 1,midg,midg; igrid,midg,midg -3.0292051E-09 1.8266844E-09 gauss-seidel spectral radius is 0.9845982 estimated iterations to convergence 66 setup time was (sec) 0.9500000 now iterating at: 14:09:00 rms-change max change #iterations 0.1240682 16.56958 at 10iterations 9.8675936E-03 1.325119 at 20iterations 9.5502165E-04 0.1184731 at 30iterations 2.0143272E-04 2.3670673E-02 at 40iterations 7.2608811E-05 9.3784332E-03 at 50iterations finished qdiffx linear iterations at : 14:09:04 total time elapsed so far: 4.570000 # loops : 50 mean,max change (kT/e) : 7.2608811E-05 9.3784332E-03 energy calculations done at 4.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.790000 DelPhi exited at 14:09:05 4.796u 0.414s 0:05.55 93.6% 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 Mon Oct 10 2011 at 14:09:05 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4471 !!! WARNING: HIQ 440 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.730760 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): -25.56000 35.10500 ymin,ymax (A): 37.76000 99.46700 zmin,zma (A): 30.54600 89.67400 x,y,z range (A): 60.66500 61.70700 59.12800 scale (grids/A): 1.730760 object centre (A): 4.772500 68.61350 60.11000 number of atom coordinates read : 4471 total number of charged atoms : 4317 net assigned charge : -2.985957 assigned positive charge : 674.3522 centred at (gu) : 90.60314 83.18184 85.75478 assigned negative charge : -677.3412 centred at (gu) : 90.35761 83.44099 86.04375 start vw surface at 0.2000000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 106309 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33445 grid for indexing accessible points = 1.400000 m= 36422 mr = 77882 m= 4655 mr = 27092 m= 193 mr = 2950 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 2447 time to turn everything in is 1.030000 number of dielectric boundary points 39616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 327 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 33466 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) : 0.5769200 object centre at (A) : 4.772500 68.61350 60.11000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5357159E-03 -2.5526568E-02 midg,1,midg; midg,igrid,midg 4.0953223E-02 4.7783452E-04 1,midg,midg; igrid,midg,midg -7.0789950E-03 3.0848391E-02 gauss-seidel spectral radius is 0.9985107 estimated iterations to convergence 205 setup time was (sec) 1.370000 now iterating at: 14:09:06 rms-change max change #iterations 4.797841 178.1812 at 10iterations 2.171391 60.55101 at 20iterations 0.9843857 27.06266 at 30iterations 0.4473426 14.01833 at 40iterations 0.2031203 5.703440 at 50iterations 9.2352569E-02 2.407715 at 60iterations 4.1851711E-02 1.219616 at 70iterations 1.9105915E-02 0.5035267 at 80iterations 8.6762020E-03 0.2486553 at 90iterations 3.9764903E-03 0.1011047 at 100iterations 1.8233183E-03 5.4008484E-02 at 110iterations 8.5689512E-04 2.4701834E-02 at 120iterations finished qdiffx linear iterations at : 14:09:16 total time elapsed so far: 11.08000 # loops : 120 mean,max change (kT/e) : 8.5689512E-04 2.4701834E-02 energy calculations done at 11.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.30000 DelPhi exited at 14:09:17 11.309u 0.485s 0:12.29 95.8% 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 Mon Oct 10 2011 at 14:09:17 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4471 !!! WARNING: HIQ 440 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.596140 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): -25.56000 35.10500 ymin,ymax (A): 37.76000 99.46700 zmin,zma (A): 30.54600 89.67400 x,y,z range (A): 60.66500 61.70700 59.12800 scale (grids/A): 2.596140 object centre (A): 4.772500 68.61350 60.11000 number of atom coordinates read : 4471 total number of charged atoms : 4317 net assigned charge : -2.985957 assigned positive charge : 674.3522 centred at (gu) : 90.90443 79.77259 83.63185 assigned negative charge : -677.3412 centred at (gu) : 90.53626 80.16134 84.06554 start vw surface at 0.2000000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 247471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33445 grid for indexing accessible points = 1.400000 m= 123363 mr = 188934 m= 39344 mr = 102566 m= 8058 mr = 31608 m= 821 mr = 6119 m= 20 mr = 510 m= 0 mr = 2 time to grow re-entrant surface = 1.660000 no. cavity mid-points inaccessible to solvent = 8438 time to turn everything in is 2.690000 number of dielectric boundary points 89338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 2.860000 number of grid points assigned charge 34520 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) : 1.730760 object centre at (A) : 4.772500 68.61350 60.11000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1068887 -0.3024470 midg,1,midg; midg,igrid,midg 0.5914505 0.2407112 1,midg,midg; igrid,midg,midg -0.2453425 0.2926545 gauss-seidel spectral radius is 0.9992514 estimated iterations to convergence 288 setup time was (sec) 3.070000 now iterating at: 14:09:20 rms-change max change #iterations 11.69163 312.5490 at 10iterations 6.847609 134.0502 at 20iterations 3.967607 71.29517 at 30iterations 2.303087 37.76057 at 40iterations 1.327231 23.23437 at 50iterations 0.7659087 12.16443 at 60iterations 0.4416047 7.337723 at 70iterations 0.2536489 4.103827 at 80iterations 0.1459324 2.384354 at 90iterations 8.3714157E-02 1.403328 at 100iterations 4.8197731E-02 0.7328825 at 110iterations 2.7735243E-02 0.4385843 at 120iterations 1.5974402E-02 0.2421627 at 130iterations 9.2252372E-03 0.1446724 at 140iterations 5.3483681E-03 9.0281844E-02 at 150iterations 3.1373107E-03 5.1725388E-02 at 160iterations 1.8745931E-03 3.1846046E-02 at 170iterations 1.1565523E-03 1.8633842E-02 at 180iterations finished qdiffx linear iterations at : 14:09:37 total time elapsed so far: 19.58000 # loops : 180 mean,max change (kT/e) : 1.1565523E-03 1.8633842E-02 energy calculations done at 19.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.81000 DelPhi exited at 14:09:38 19.813u 0.530s 0:20.68 98.3% 0+0k 0+0io 0pf+0w