Sun Oct 9 17:14:08 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 Sun Oct 9 2011 at 17:14:08 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5258 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5483503 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): 3.230000 68.15200 ymin,ymax (A): -8.582000 53.48700 zmin,zma (A): -1.171000 61.97800 x,y,z range (A): 64.92200 62.06900 63.14900 scale (grids/A): 0.5483503 object centre (A): 35.69100 22.45250 30.40350 number of atom coordinates read : 5258 total number of charged atoms : 5114 net assigned charge : 0.6350498 assigned positive charge : 813.0443 centred at (gu) : 88.22755 89.16258 89.47392 assigned negative charge : -812.4155 centred at (gu) : 88.10789 89.21468 89.42156 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 10300 nv = 96 ne = 84 npr = 106543 no. pairs analyzed = 106543 no. exposed pairs = 6150 no. arc points = 41668 no. surface atoms = 2099 nbur = 3159 mkacc time = 0.2400000 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 = 1.568000 m= 441 mr = 5878 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4260 ## 504 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 13549 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.1045869E-10 6.6617295E-10 midg,1,midg; midg,igrid,midg 9.3333241E-10 -5.0156573E-10 1,midg,midg; igrid,midg,midg -2.3999946E-09 1.0500539E-09 gauss-seidel spectral radius is 0.9830150 estimated iterations to convergence 63 setup time was (sec) 0.7800000 now iterating at: 17:14:09 rms-change max change #iterations 0.1073774 13.88671 at 10iterations 9.4152987E-03 1.204777 at 20iterations 2.7245169E-03 0.3118973 at 30iterations 1.2774649E-03 0.1368179 at 40iterations 6.2522013E-04 6.9762230E-02 at 50iterations finished qdiffx linear iterations at : 17:14:12 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 6.2522013E-04 6.9762230E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 17:14:12 3.628u 0.126s 0:04.02 93.0% 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 Sun Oct 9 2011 at 17:14:12 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5258 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.645051 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): 3.230000 68.15200 ymin,ymax (A): -8.582000 53.48700 zmin,zma (A): -1.171000 61.97800 x,y,z range (A): 64.92200 62.06900 63.14900 scale (grids/A): 1.645051 object centre (A): 35.69100 22.45250 30.40350 number of atom coordinates read : 5258 total number of charged atoms : 5114 net assigned charge : 0.6350498 assigned positive charge : 813.0443 centred at (gu) : 84.68132 87.48674 88.42024 assigned negative charge : -812.4155 centred at (gu) : 84.32380 87.64375 88.26478 start vw surface at 0.2200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 114812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41668 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 39536 mr = 83300 m= 4694 mr = 28459 m= 138 mr = 2506 m= 0 mr = 12 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8100000 number of dielectric boundary points 44903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 395 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 39194 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) : 0.5483503 object centre at (A) : 35.69100 22.45250 30.40350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5592765E-02 -9.4143646E-03 midg,1,midg; midg,igrid,midg 1.6958326E-02 7.9901377E-03 1,midg,midg; igrid,midg,midg -2.3076020E-02 7.0004007E-03 gauss-seidel spectral radius is 0.9984171 estimated iterations to convergence 199 setup time was (sec) 1.100000 now iterating at: 17:14:13 rms-change max change #iterations 4.832728 193.9547 at 10iterations 2.135885 58.60176 at 20iterations 0.9459885 25.99207 at 30iterations 0.4189102 12.62946 at 40iterations 0.1864924 5.649071 at 50iterations 8.2650453E-02 2.114219 at 60iterations 3.7104651E-02 1.053280 at 70iterations 1.6981067E-02 0.5271873 at 80iterations 8.2947342E-03 0.2382851 at 90iterations 4.4921972E-03 0.1217155 at 100iterations 2.8092081E-03 7.3425293E-02 at 110iterations 1.9806409E-03 4.7894478E-02 at 120iterations finished qdiffx linear iterations at : 17:14:20 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 1.9806409E-03 4.7894478E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 17:14:21 8.002u 0.175s 0:08.49 96.2% 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 Sun Oct 9 2011 at 17:14:21 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5258 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.467577 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): 3.230000 68.15200 ymin,ymax (A): -8.582000 53.48700 zmin,zma (A): -1.171000 61.97800 x,y,z range (A): 64.92200 62.06900 63.14900 scale (grids/A): 2.467577 object centre (A): 35.69100 22.45250 30.40350 number of atom coordinates read : 5258 total number of charged atoms : 5114 net assigned charge : 0.6350498 assigned positive charge : 813.0443 centred at (gu) : 82.02156 86.22971 87.62992 assigned negative charge : -812.4155 centred at (gu) : 81.48563 86.46555 87.39715 start vw surface at 0.2200000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 267008 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41668 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 133812 mr = 202740 m= 41663 mr = 108987 m= 7506 mr = 32293 m= 661 mr = 5139 m= 10 mr = 328 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.040000 number of dielectric boundary points 101173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 51 iepsmp to db, and charging done at 2.190000 number of grid points assigned charge 40880 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) : 1.645051 object centre at (A) : 35.69100 22.45250 30.40350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3914295 -0.2942793 midg,1,midg; midg,igrid,midg 8.3420262E-02 -4.3947469E-03 1,midg,midg; igrid,midg,midg -0.4676975 0.1126637 gauss-seidel spectral radius is 0.9992515 estimated iterations to convergence 288 setup time was (sec) 2.350000 now iterating at: 17:14:23 rms-change max change #iterations 12.27642 311.9261 at 10iterations 7.229675 185.7443 at 20iterations 4.221003 81.28793 at 30iterations 2.458799 43.73379 at 40iterations 1.425890 25.56667 at 50iterations 0.8250924 14.05915 at 60iterations 0.4771305 7.509335 at 70iterations 0.2751920 4.515592 at 80iterations 0.1586263 2.693488 at 90iterations 9.1499031E-02 1.360550 at 100iterations 5.2788291E-02 0.8220778 at 110iterations 3.0537849E-02 0.5117302 at 120iterations 1.7850522E-02 0.2836227 at 130iterations 1.0619379E-02 0.1867065 at 140iterations 6.5214331E-03 0.1105013 at 150iterations 4.2087277E-03 6.8817139E-02 at 160iterations 2.9284216E-03 4.7225952E-02 at 170iterations 2.1900625E-03 3.3515930E-02 at 180iterations finished qdiffx linear iterations at : 17:14:34 total time elapsed so far: 13.06000 # loops : 180 mean,max change (kT/e) : 2.1900625E-03 3.3515930E-02 energy calculations done at 13.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.25000 DelPhi exited at 17:14:34 13.249u 0.181s 0:13.70 97.9% 0+0k 0+0io 0pf+0w