Fri Aug 1 15:18:56 PDT 2008 #!/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 Fri Aug 1 2008 at 15:18:56 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: 17 atomic charges read from file fort.12 # of charge parameter records: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 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: 0.5725774 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 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): -13.88300 48.29200 ymin,ymax (A): -27.17500 25.34100 zmin,zma (A): -29.86900 30.00800 x,y,z range (A): 62.17500 52.51600 59.87700 scale (grids/A): 0.5725774 object centre (A): 17.20450 -0.9169998 6.9499969E-02 number of atom coordinates read : 2770 total number of charged atoms : 2633 net assigned charge : 6.000010 assigned positive charge : 395.6485 centred at (gu) : 89.50247 89.74668 91.14146 assigned negative charge : -389.6495 centred at (gu) : 89.88327 90.06700 91.02235 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5906 nv = 96 ne = 84 npr = 59156 no. pairs analyzed = 59156 no. exposed pairs = 3900 no. arc points = 27222 no. surface atoms = 1322 nbur = 1448 mkacc time = 0.1700000 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 = 1.512000 m= 277 mr = 2543 m= 0 mr = 11 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2783 ## 269 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7607 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1561324E-08 8.3642085E-08 midg,1,midg; midg,igrid,midg 1.3923184E-07 -8.2448416E-08 1,midg,midg; igrid,midg,midg 1.6760174E-07 -9.8437951E-08 gauss-seidel spectral radius is 0.9890049 estimated iterations to convergence 78 setup time was (sec) 0.6300000 now iterating at: 15:18:57 rms-change max change #iterations 0.1265361 20.21854 at 10iterations 1.4988480E-02 2.559140 at 20iterations 2.2648489E-03 0.4311600 at 30iterations 5.5975589E-04 0.1101990 at 40iterations 1.7999043E-04 3.6697388E-02 at 50iterations finished qdiffx linear iterations at : 15:19:00 total time elapsed so far: 3.720000 # loops : 50 mean,max change (kT/e) : 1.7999043E-04 3.6697388E-02 energy calculations done at 3.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.880000 DelPhi exited at 15:19:01 3.887u 0.282s 0:05.02 82.8% 0+0k 0+45928io 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 Fri Aug 1 2008 at 15:19:01 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: 17 atomic charges read from file fort.12 # of charge parameter records: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 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: 1.717732 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 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): -13.88300 48.29200 ymin,ymax (A): -27.17500 25.34100 zmin,zma (A): -29.86900 30.00800 x,y,z range (A): 62.17500 52.51600 59.87700 scale (grids/A): 1.717732 object centre (A): 17.20450 -0.9169998 6.9499969E-02 number of atom coordinates read : 2770 total number of charged atoms : 2633 net assigned charge : 6.000010 assigned positive charge : 395.6485 centred at (gu) : 88.50665 89.23910 93.42389 assigned negative charge : -389.6495 centred at (gu) : 89.64938 90.20086 93.06664 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 63714 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27222 grid for indexing accessible points = 1.400000 m= 19329 mr = 39265 m= 2568 mr = 12009 m= 100 mr = 1137 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 33283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 221 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20417 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) : 0.5725774 object centre at (A) : 17.20450 -0.9169998 6.9499969E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5930082E-03 2.5944432E-02 midg,1,midg; midg,igrid,midg 7.4755318E-02 -2.1797402E-02 1,midg,midg; igrid,midg,midg 8.2306899E-02 -6.7200787E-02 gauss-seidel spectral radius is 0.9987324 estimated iterations to convergence 222 setup time was (sec) 0.9200000 now iterating at: 15:19:03 rms-change max change #iterations 3.908998 188.5409 at 10iterations 1.879264 76.51414 at 20iterations 0.9014808 37.32270 at 30iterations 0.4332683 18.42760 at 40iterations 0.2085084 7.061152 at 50iterations 0.1003402 3.638657 at 60iterations 4.8434649E-02 1.724997 at 70iterations 2.3341641E-02 0.9568367 at 80iterations 1.1370693E-02 0.4155655 at 90iterations 5.6200265E-03 0.2101822 at 100iterations 2.8584015E-03 0.1241684 at 110iterations 1.5299693E-03 5.9288025E-02 at 120iterations finished qdiffx linear iterations at : 15:19:10 total time elapsed so far: 8.780000 # loops : 120 mean,max change (kT/e) : 1.5299693E-03 5.9288025E-02 energy calculations done at 8.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.950000 DelPhi exited at 15:19:11 8.950u 0.362s 0:09.99 93.1% 0+0k 45472+45272io 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 Fri Aug 1 2008 at 15:19:11 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: 17 atomic charges read from file fort.12 # of charge parameter records: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 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: 2.576598 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 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): -13.88300 48.29200 ymin,ymax (A): -27.17500 25.34100 zmin,zma (A): -29.86900 30.00800 x,y,z range (A): 62.17500 52.51600 59.87700 scale (grids/A): 2.576598 object centre (A): 17.20450 -0.9169998 6.9499969E-02 number of atom coordinates read : 2770 total number of charged atoms : 2633 net assigned charge : 6.000010 assigned positive charge : 395.6485 centred at (gu) : 87.75974 88.85848 95.13560 assigned negative charge : -389.6495 centred at (gu) : 89.47395 90.30115 94.59987 start vw surface at 0.1500000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 147599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27222 grid for indexing accessible points = 1.400000 m= 64402 mr = 97494 m= 20445 mr = 47502 m= 4117 mr = 14307 m= 441 mr = 2553 m= 13 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 0.9200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 74967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 21051 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) : 1.717732 object centre at (A) : 17.20450 -0.9169998 6.9499969E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7433608E-02 0.2333156 midg,1,midg; midg,igrid,midg 0.5321348 -0.1822672 1,midg,midg; igrid,midg,midg 0.7380404 -0.9212813 gauss-seidel spectral radius is 0.9992785 estimated iterations to convergence 294 setup time was (sec) 1.890000 now iterating at: 15:19:14 rms-change max change #iterations 9.160444 322.8647 at 10iterations 5.407168 147.7331 at 20iterations 3.160963 69.20682 at 30iterations 1.845123 43.17968 at 40iterations 1.072271 24.25595 at 50iterations 0.6228352 14.93132 at 60iterations 0.3615006 7.941973 at 70iterations 0.2095076 4.759294 at 80iterations 0.1213841 2.637345 at 90iterations 7.0208371E-02 1.480669 at 100iterations 4.0565938E-02 0.8355312 at 110iterations 2.3518829E-02 0.4744759 at 120iterations 1.3653893E-02 0.2991867 at 130iterations 7.9661878E-03 0.1583710 at 140iterations 4.6608336E-03 0.1004906 at 150iterations 2.7773255E-03 6.5277100E-02 at 160iterations 1.6975809E-03 4.1339874E-02 at 170iterations 1.0919485E-03 2.5951385E-02 at 180iterations finished qdiffx linear iterations at : 15:19:27 total time elapsed so far: 14.96000 # loops : 180 mean,max change (kT/e) : 1.0919485E-03 2.5951385E-02 energy calculations done at 14.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.12000 DelPhi exited at 15:19:27 15.129u 0.436s 0:16.06 96.8% 0+0k 44808+45264io 0pf+0w