Sat Oct 8 18:08:57 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 Sat Oct 8 2011 at 18:08:57 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4414 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5221549 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): -29.69900 38.48000 ymin,ymax (A): -17.56300 41.31600 zmin,zma (A): -5.834000 60.24200 x,y,z range (A): 68.17900 58.87900 66.07600 scale (grids/A): 0.5221549 object centre (A): 4.390501 11.87650 27.20400 number of atom coordinates read : 4414 total number of charged atoms : 4262 net assigned charge : -6.999974 assigned positive charge : 679.0333 centred at (gu) : 91.01831 91.92672 90.23650 assigned negative charge : -686.0381 centred at (gu) : 90.99741 91.97523 90.21365 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7853 nv = 96 ne = 84 npr = 86005 no. pairs analyzed = 86005 no. exposed pairs = 5924 no. arc points = 41903 no. surface atoms = 1981 nbur = 2433 mkacc time = 0.1400000 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 = 1.652000 m= 300 mr = 3842 m= 0 mr = 11 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4253 ## 646 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 10523 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3787056E-10 -7.3088174E-11 midg,1,midg; midg,igrid,midg 1.7782626E-11 -5.8844463E-10 1,midg,midg; igrid,midg,midg -1.8919698E-10 -9.8035718E-11 gauss-seidel spectral radius is 0.9812264 estimated iterations to convergence 60 setup time was (sec) 0.5000000 now iterating at: 18:08:58 rms-change max change #iterations 7.4627019E-02 10.62998 at 10iterations 4.5767748E-03 0.6296572 at 20iterations 4.1251309E-04 8.8840485E-02 at 30iterations 9.2308524E-05 1.8309593E-02 at 40iterations 2.6569398E-05 5.3720474E-03 at 50iterations finished qdiffx linear iterations at : 18:09:01 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 2.6569398E-05 5.3720474E-03 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 18:09:02 3.697u 0.204s 0:04.27 91.1% 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 Sat Oct 8 2011 at 18:09:02 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4414 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: 1.566465 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): -29.69900 38.48000 ymin,ymax (A): -17.56300 41.31600 zmin,zma (A): -5.834000 60.24200 x,y,z range (A): 68.17900 58.87900 66.07600 scale (grids/A): 1.566465 object centre (A): 4.390501 11.87650 27.20400 number of atom coordinates read : 4414 total number of charged atoms : 4262 net assigned charge : -6.999974 assigned positive charge : 679.0333 centred at (gu) : 93.05368 95.77849 90.70782 assigned negative charge : -686.0381 centred at (gu) : 92.99189 95.92559 90.64098 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 87447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41903 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 25619 mr = 57518 m= 2318 mr = 16686 m= 59 mr = 971 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 198 time to turn everything in is 0.4400000 number of dielectric boundary points 40268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 582 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 32309 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) : 0.5221549 object centre at (A) : 4.390501 11.87650 27.20400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7046989E-03 -2.4078484E-03 midg,1,midg; midg,igrid,midg -5.5998801E-03 -1.3816060E-02 1,midg,midg; igrid,midg,midg -4.8434427E-03 4.5067482E-03 gauss-seidel spectral radius is 0.9981717 estimated iterations to convergence 186 setup time was (sec) 0.6900000 now iterating at: 18:09:03 rms-change max change #iterations 3.874175 174.0205 at 10iterations 1.603156 54.91138 at 20iterations 0.6634552 23.78209 at 30iterations 0.2751060 10.59708 at 40iterations 0.1140888 3.627132 at 50iterations 4.7408748E-02 1.766640 at 60iterations 1.9672308E-02 0.6269684 at 70iterations 8.2538659E-03 0.2598267 at 80iterations 3.4634548E-03 0.1138763 at 90iterations 1.4708489E-03 5.1644325E-02 at 100iterations 6.4674357E-04 2.3513794E-02 at 110iterations 3.0161938E-04 1.0883451E-02 at 120iterations finished qdiffx linear iterations at : 18:09:10 total time elapsed so far: 8.290000 # loops : 120 mean,max change (kT/e) : 3.0161938E-04 1.0883451E-02 energy calculations done at 8.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.430000 DelPhi exited at 18:09:11 8.428u 0.218s 0:08.92 96.7% 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 Sat Oct 8 2011 at 18:09:11 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: 18 atomic charges read from file fort.12 # of charge parameter records: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4414 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.349697 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): -29.69900 38.48000 ymin,ymax (A): -17.56300 41.31600 zmin,zma (A): -5.834000 60.24200 x,y,z range (A): 68.17900 58.87900 66.07600 scale (grids/A): 2.349697 object centre (A): 4.390501 11.87650 27.20400 number of atom coordinates read : 4414 total number of charged atoms : 4262 net assigned charge : -6.999974 assigned positive charge : 679.0333 centred at (gu) : 94.58028 98.66739 91.06174 assigned negative charge : -686.0381 centred at (gu) : 94.48777 98.88830 90.96127 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 203697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41903 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 90772 mr = 141993 m= 23393 mr = 69874 m= 3198 mr = 16606 m= 191 mr = 1819 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 659 time to turn everything in is 1.050000 number of dielectric boundary points 90902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 34029 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) : 1.566465 object centre at (A) : 4.390501 11.87650 27.20400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1489277 -1.6165877E-02 midg,1,midg; midg,igrid,midg -5.9303816E-02 -0.1941466 1,midg,midg; igrid,midg,midg -7.7274062E-02 3.5480410E-02 gauss-seidel spectral radius is 0.9991640 estimated iterations to convergence 273 setup time was (sec) 1.300000 now iterating at: 18:09:12 rms-change max change #iterations 10.38347 291.8110 at 10iterations 5.962870 134.2369 at 20iterations 3.398253 80.99586 at 30iterations 1.922587 37.94075 at 40iterations 1.081852 25.98059 at 50iterations 0.6080453 13.31398 at 60iterations 0.3401893 7.296082 at 70iterations 0.1901794 3.578667 at 80iterations 0.1058832 2.005043 at 90iterations 5.9100233E-02 1.110287 at 100iterations 3.2934424E-02 0.5952301 at 110iterations 1.8324841E-02 0.3707886 at 120iterations 1.0191862E-02 0.1773019 at 130iterations 5.6703775E-03 0.1072102 at 140iterations 3.1607179E-03 6.2077761E-02 at 150iterations 1.7647715E-03 3.2032013E-02 at 160iterations 9.9195458E-04 1.7356873E-02 at 170iterations 5.6133582E-04 1.0684967E-02 at 180iterations finished qdiffx linear iterations at : 18:09:25 total time elapsed so far: 13.62000 # loops : 180 mean,max change (kT/e) : 5.6133582E-04 1.0684967E-02 energy calculations done at 13.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.76000 DelPhi exited at 18:09:25 13.758u 0.258s 0:14.29 97.9% 0+0k 0+0io 0pf+0w