Wed Feb 15 08:57:43 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:57:43 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 ! Automatically converted by prot2crg.py # of charge parameter records: 936 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5496 !!! WARNING: ZN1 990 has a net charge of 1.4000 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: 0.5287312 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): -18.85600 48.47500 ymin,ymax (A): -58.39800 6.901000 zmin,zma (A): -29.95400 32.85400 x,y,z range (A): 67.33100 65.29900 62.80800 scale (grids/A): 0.5287312 object centre (A): 14.80950 -25.74850 1.450000 number of atom coordinates read : 5496 total number of charged atoms : 5324 net assigned charge : -10.60001 assigned positive charge : 844.5702 centred at (gu) : 89.63299 90.12318 91.51485 assigned negative charge : -855.1769 centred at (gu) : 89.70992 90.12177 91.52689 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 9549 nv = 96 ne = 84 npr = 113140 no. pairs analyzed = 113140 no. exposed pairs = 6537 no. arc points = 45193 no. surface atoms = 2185 nbur = 3311 mkacc time = 0.2600000 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= 339 mr = 5181 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.5200000 number of dielectric boundary points 4695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4396 ## 594 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 12839 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7330810E-10 -5.9736754E-10 midg,1,midg; midg,igrid,midg -3.2777003E-10 -3.2942968E-10 1,midg,midg; igrid,midg,midg 1.8883931E-10 -7.6317219E-10 gauss-seidel spectral radius is 0.9817449 estimated iterations to convergence 61 setup time was (sec) 0.7400000 now iterating at: 08:57:44 rms-change max change #iterations 8.3426736E-02 11.18315 at 10iterations 5.2829687E-03 0.8970351 at 20iterations 3.9658198E-04 5.3752899E-02 at 30iterations 6.3745807E-05 7.2326660E-03 at 40iterations 1.6531292E-05 1.9721985E-03 at 50iterations finished qdiffx linear iterations at : 08:57:47 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.6531292E-05 1.9721985E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 08:57:47 3.585u 0.172s 0:04.29 87.4% 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 Wed Feb 15 2012 at 08:57:48 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 ! Automatically converted by prot2crg.py # of charge parameter records: 936 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5496 !!! WARNING: ZN1 990 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.586194 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): -18.85600 48.47500 ymin,ymax (A): -58.39800 6.901000 zmin,zma (A): -29.95400 32.85400 x,y,z range (A): 67.33100 65.29900 62.80800 scale (grids/A): 1.586194 object centre (A): 14.80950 -25.74850 1.450000 number of atom coordinates read : 5496 total number of charged atoms : 5324 net assigned charge : -10.60001 assigned positive charge : 844.5702 centred at (gu) : 88.89735 90.36765 94.54298 assigned negative charge : -855.1769 centred at (gu) : 89.12975 90.36486 94.58053 start vw surface at 0.2700000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 108961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45193 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 32459 mr = 77198 m= 3063 mr = 22194 m= 91 mr = 1375 m= 0 mr = 6 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2962 time to turn everything in is 0.8300000 number of dielectric boundary points 43801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 497 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 40348 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) : 0.5287312 object centre at (A) : 14.80950 -25.74850 1.450000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8113308E-02 -2.1103865E-02 midg,1,midg; midg,igrid,midg -1.3900660E-02 -2.1936065E-02 1,midg,midg; igrid,midg,midg 2.7966350E-03 -8.4338570E-03 gauss-seidel spectral radius is 0.9983069 estimated iterations to convergence 193 setup time was (sec) 1.120000 now iterating at: 08:57:49 rms-change max change #iterations 4.534907 170.9820 at 10iterations 1.954792 73.96114 at 20iterations 0.8397686 24.49781 at 30iterations 0.3609442 10.28031 at 40iterations 0.1557085 4.556652 at 50iterations 6.7436092E-02 1.854467 at 60iterations 2.8957123E-02 0.8445755 at 70iterations 1.2479129E-02 0.3509445 at 80iterations 5.3768232E-03 0.1500320 at 90iterations 2.3283393E-03 7.5706482E-02 at 100iterations 1.0070457E-03 3.3588409E-02 at 110iterations 4.3561269E-04 1.3168335E-02 at 120iterations finished qdiffx linear iterations at : 08:57:55 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 4.3561269E-04 1.3168335E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 08:57:56 7.938u 0.184s 0:08.45 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 Wed Feb 15 2012 at 08:57:56 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 ! Automatically converted by prot2crg.py # of charge parameter records: 936 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5496 !!! WARNING: ZN1 990 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.379290 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): -18.85600 48.47500 ymin,ymax (A): -58.39800 6.901000 zmin,zma (A): -29.95400 32.85400 x,y,z range (A): 67.33100 65.29900 62.80800 scale (grids/A): 2.379290 object centre (A): 14.80950 -25.74850 1.450000 number of atom coordinates read : 5496 total number of charged atoms : 5324 net assigned charge : -10.60001 assigned positive charge : 844.5702 centred at (gu) : 88.34577 90.55129 96.81423 assigned negative charge : -855.1769 centred at (gu) : 88.69469 90.54723 96.87064 start vw surface at 0.2300000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 254502 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45193 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 114918 mr = 188996 m= 30355 mr = 91353 m= 4675 mr = 22441 m= 298 mr = 2950 m= 5 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 9907 time to turn everything in is 1.860000 number of dielectric boundary points 98920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 42528 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) : 1.586194 object centre at (A) : 14.80950 -25.74850 1.450000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3383858 -0.2703501 midg,1,midg; midg,igrid,midg -0.1388459 -0.4115923 1,midg,midg; igrid,midg,midg 0.1209445 3.8561549E-02 gauss-seidel spectral radius is 0.9992272 estimated iterations to convergence 284 setup time was (sec) 2.180000 now iterating at: 08:57:58 rms-change max change #iterations 11.94752 301.0000 at 10iterations 7.012732 148.4099 at 20iterations 4.061918 92.30148 at 30iterations 2.347023 45.55950 at 40iterations 1.350070 24.38108 at 50iterations 0.7745497 16.73383 at 60iterations 0.4436343 7.429269 at 70iterations 0.2535812 4.368828 at 80iterations 0.1446918 2.351189 at 90iterations 8.2518086E-02 1.437324 at 100iterations 4.7001794E-02 0.7773781 at 110iterations 2.6718054E-02 0.4529443 at 120iterations 1.5216486E-02 0.2444267 at 130iterations 8.6624790E-03 0.1480560 at 140iterations 4.9235509E-03 8.6003304E-02 at 150iterations 2.7971524E-03 4.6169281E-02 at 160iterations 1.5909533E-03 2.6317596E-02 at 170iterations 9.0411637E-04 1.4022827E-02 at 180iterations finished qdiffx linear iterations at : 08:58:10 total time elapsed so far: 14.22000 # loops : 180 mean,max change (kT/e) : 9.0411637E-04 1.4022827E-02 energy calculations done at 14.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.43000 DelPhi exited at 08:58:11 14.428u 0.216s 0:15.41 94.9% 0+0k 0+0io 0pf+0w