Mon Oct 10 17:07:59 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+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 Mon Oct 10 2011 at 17:07:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3014 !!! WARNING: PRO 352 has a net charge of 0.5000 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: 0.5486630 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): -2.475000 62.41000 ymin,ymax (A): 48.89600 97.55099 zmin,zma (A): -9.618000 36.28000 x,y,z range (A): 64.88500 48.65499 45.89800 scale (grids/A): 0.5486630 object centre (A): 29.96750 73.22350 13.33100 number of atom coordinates read : 3014 total number of charged atoms : 2873 net assigned charge : 1.000021 assigned positive charge : 448.9468 centred at (gu) : 89.60701 90.37389 90.28520 assigned negative charge : -447.9481 centred at (gu) : 89.61488 90.46233 90.18473 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5909 nv = 96 ne = 84 npr = 59981 no. pairs analyzed = 59981 no. exposed pairs = 3921 no. arc points = 28051 no. surface atoms = 1322 nbur = 1692 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 = 1.596000 m= 252 mr = 2969 m= 3 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3186 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2808 ## 358 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7774 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.3599831E-10 8.6387147E-10 midg,1,midg; midg,igrid,midg 6.5367545E-10 -6.5084432E-10 1,midg,midg; igrid,midg,midg 1.4103804E-10 1.0827388E-11 gauss-seidel spectral radius is 0.9828794 estimated iterations to convergence 63 setup time was (sec) 0.6400000 now iterating at: 17:08:00 rms-change max change #iterations 7.3000513E-02 12.18001 at 10iterations 4.9286983E-03 0.7582264 at 20iterations 3.3598734E-04 4.8933029E-02 at 30iterations 2.3011464E-05 3.6239624E-03 at 40iterations 1.5817814E-06 2.8800964E-04 at 50iterations finished qdiffx linear iterations at : 17:08:04 total time elapsed so far: 4.620000 # loops : 50 mean,max change (kT/e) : 1.5817814E-06 2.8800964E-04 energy calculations done at 4.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.790000 DelPhi exited at 17:08:05 4.793u 0.384s 0:05.46 94.6% 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 17:08:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3014 !!! WARNING: PRO 352 has a net charge of 0.5000 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: 1.645989 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): -2.475000 62.41000 ymin,ymax (A): 48.89600 97.55099 zmin,zma (A): -9.618000 36.28000 x,y,z range (A): 64.88500 48.65499 45.89800 scale (grids/A): 1.645989 object centre (A): 29.96750 73.22350 13.33100 number of atom coordinates read : 3014 total number of charged atoms : 2873 net assigned charge : 1.000021 assigned positive charge : 448.9468 centred at (gu) : 88.82021 91.12080 90.85475 assigned negative charge : -447.9481 centred at (gu) : 88.84415 91.38642 90.55377 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 65524 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28051 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19520 mr = 43488 m= 1963 mr = 13165 m= 47 mr = 948 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 198 time to turn everything in is 0.5300000 number of dielectric boundary points 29453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 319 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 22002 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) : 0.5486630 object centre at (A) : 29.96750 73.22350 13.33100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3449758E-03 5.4485141E-03 midg,1,midg; midg,igrid,midg 5.3665047E-03 -1.2095825E-02 1,midg,midg; igrid,midg,midg -4.0261415E-03 2.1800597E-03 gauss-seidel spectral radius is 0.9982212 estimated iterations to convergence 188 setup time was (sec) 0.8800000 now iterating at: 17:08:06 rms-change max change #iterations 3.360511 173.1006 at 10iterations 1.403179 57.35280 at 20iterations 0.5888016 24.40912 at 30iterations 0.2479308 8.945137 at 40iterations 0.1041636 3.645935 at 50iterations 4.3870509E-02 1.691242 at 60iterations 1.8386226E-02 0.6771717 at 70iterations 7.7390200E-03 0.2872686 at 80iterations 3.2561109E-03 0.1200227 at 90iterations 1.3679545E-03 6.0451508E-02 at 100iterations 5.7729823E-04 2.0830154E-02 at 110iterations 2.4190341E-04 8.5074902E-03 at 120iterations finished qdiffx linear iterations at : 17:08:16 total time elapsed so far: 10.97000 # loops : 120 mean,max change (kT/e) : 2.4190341E-04 8.5074902E-03 energy calculations done at 10.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.14000 DelPhi exited at 17:08:16 11.143u 0.450s 0:11.94 97.0% 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 17:08:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3014 !!! WARNING: PRO 352 has a net charge of 0.5000 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: 2.468983 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): -2.475000 62.41000 ymin,ymax (A): 48.89600 97.55099 zmin,zma (A): -9.618000 36.28000 x,y,z range (A): 64.88500 48.65499 45.89800 scale (grids/A): 2.468983 object centre (A): 29.96750 73.22350 13.33100 number of atom coordinates read : 3014 total number of charged atoms : 2873 net assigned charge : 1.000021 assigned positive charge : 448.9468 centred at (gu) : 88.23009 91.68082 91.28202 assigned negative charge : -447.9481 centred at (gu) : 88.26614 92.07953 90.83044 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 152103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28051 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 67436 mr = 106644 m= 19411 mr = 52490 m= 3005 mr = 14502 m= 182 mr = 1905 m= 1 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 632 time to turn everything in is 1.310000 number of dielectric boundary points 66527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 22954 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) : 1.645989 object centre at (A) : 29.96750 73.22350 13.33100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9879930E-02 6.8912692E-02 midg,1,midg; midg,igrid,midg 9.3020655E-02 -0.1935139 1,midg,midg; igrid,midg,midg -0.2255060 6.8250537E-02 gauss-seidel spectral radius is 0.9991532 estimated iterations to convergence 271 setup time was (sec) 1.670000 now iterating at: 17:08:19 rms-change max change #iterations 8.814534 290.9001 at 10iterations 4.966360 143.4671 at 20iterations 2.784497 63.08590 at 30iterations 1.552217 36.93089 at 40iterations 0.8660854 17.77301 at 50iterations 0.4803641 10.86180 at 60iterations 0.2664249 5.937504 at 70iterations 0.1472926 3.321289 at 80iterations 8.1753068E-02 1.718786 at 90iterations 4.5108464E-02 1.095266 at 100iterations 2.4914071E-02 0.5902786 at 110iterations 1.3762267E-02 0.2818375 at 120iterations 7.5990595E-03 0.1594276 at 130iterations 4.2036264E-03 8.1340790E-02 at 140iterations 2.3186791E-03 4.6854019E-02 at 150iterations 1.2777448E-03 2.8605461E-02 at 160iterations 7.0502952E-04 1.6923904E-02 at 170iterations 3.8948559E-04 8.7127686E-03 at 180iterations finished qdiffx linear iterations at : 17:08:36 total time elapsed so far: 19.28000 # loops : 180 mean,max change (kT/e) : 3.8948559E-04 8.7127686E-03 energy calculations done at 19.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.44000 DelPhi exited at 17:08:37 19.448u 0.464s 0:20.18 98.6% 0+0k 0+0io 0pf+0w