Tue Oct 11 07:38:13 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 Tue Oct 11 2011 at 07:38:13 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3304 !!! WARNING: UMP 1125 has a net charge of -0.1000 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: 0.6034614 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): 1.431000 52.53800 ymin,ymax (A): 0.8570000 59.85000 zmin,zma (A): -22.35700 35.72700 x,y,z range (A): 51.10700 58.99300 58.08400 scale (grids/A): 0.6034614 object centre (A): 26.98450 30.35350 6.684999 number of atom coordinates read : 3304 total number of charged atoms : 3162 net assigned charge : 6.900036 assigned positive charge : 500.0456 centred at (gu) : 90.18733 90.57532 89.24602 assigned negative charge : -493.1471 centred at (gu) : 90.20982 90.53123 89.13017 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8188 nv = 96 ne = 84 npr = 66280 no. pairs analyzed = 66280 no. exposed pairs = 4043 no. arc points = 28105 no. surface atoms = 1361 nbur = 1943 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 = 1.456000 m= 425 mr = 4605 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2896 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10102 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2571807E-09 7.8004581E-09 midg,1,midg; midg,igrid,midg 9.5089603E-10 6.3800640E-09 1,midg,midg; igrid,midg,midg 4.3208979E-09 2.2732671E-09 gauss-seidel spectral radius is 0.9858485 estimated iterations to convergence 69 setup time was (sec) 0.6600000 now iterating at: 07:38:14 rms-change max change #iterations 0.1274139 23.76891 at 10iterations 1.1346227E-02 1.440436 at 20iterations 1.5669325E-03 0.2315826 at 30iterations 4.5428879E-04 7.1710110E-02 at 40iterations 1.6454974E-04 2.6107311E-02 at 50iterations finished qdiffx linear iterations at : 07:38:17 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 1.6454974E-04 2.6107311E-02 energy calculations done at 4.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 07:38:18 4.555u 0.388s 0:05.50 89.6% 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 Tue Oct 11 2011 at 07:38:18 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3304 !!! WARNING: UMP 1125 has a net charge of -0.1000 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: 1.810384 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): 1.431000 52.53800 ymin,ymax (A): 0.8570000 59.85000 zmin,zma (A): -22.35700 35.72700 x,y,z range (A): 51.10700 58.99300 58.08400 scale (grids/A): 1.810384 object centre (A): 26.98450 30.35350 6.684999 number of atom coordinates read : 3304 total number of charged atoms : 3162 net assigned charge : 6.900036 assigned positive charge : 500.0456 centred at (gu) : 90.56065 91.72496 87.73748 assigned negative charge : -493.1471 centred at (gu) : 90.62901 91.59351 87.39014 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 89460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28105 grid for indexing accessible points = 1.400000 m= 33729 mr = 63280 m= 5065 mr = 25327 m= 211 mr = 3169 m= 0 mr = 42 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 362 time to turn everything in is 0.7300000 number of dielectric boundary points 36647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 24711 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) : 0.6034614 object centre at (A) : 26.98450 30.35350 6.684999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5274211E-02 1.7325910E-02 midg,1,midg; midg,igrid,midg 1.8421244E-02 5.2828030E-03 1,midg,midg; igrid,midg,midg 2.8030742E-02 1.2983840E-02 gauss-seidel spectral radius is 0.9985722 estimated iterations to convergence 210 setup time was (sec) 1.080000 now iterating at: 07:38:20 rms-change max change #iterations 4.435748 200.3969 at 10iterations 2.038785 63.09010 at 20iterations 0.9426468 30.24326 at 30iterations 0.4356446 13.07286 at 40iterations 0.2007670 6.323605 at 50iterations 9.2963465E-02 3.022331 at 60iterations 4.3106247E-02 1.335674 at 70iterations 2.0073520E-02 0.6106725 at 80iterations 9.4070677E-03 0.2726851 at 90iterations 4.4955737E-03 0.1490355 at 100iterations 2.2426520E-03 7.7661514E-02 at 110iterations 1.1987281E-03 4.5814514E-02 at 120iterations finished qdiffx linear iterations at : 07:38:30 total time elapsed so far: 11.18000 # loops : 120 mean,max change (kT/e) : 1.1987281E-03 4.5814514E-02 energy calculations done at 11.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.34000 DelPhi exited at 07:38:31 11.344u 0.464s 0:12.44 94.8% 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 Tue Oct 11 2011 at 07:38:31 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3304 !!! WARNING: UMP 1125 has a net charge of -0.1000 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: 2.715576 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): 1.431000 52.53800 ymin,ymax (A): 0.8570000 59.85000 zmin,zma (A): -22.35700 35.72700 x,y,z range (A): 51.10700 58.99300 58.08400 scale (grids/A): 2.715576 object centre (A): 26.98450 30.35350 6.684999 number of atom coordinates read : 3304 total number of charged atoms : 3162 net assigned charge : 6.900036 assigned positive charge : 500.0456 centred at (gu) : 90.84077 92.58727 86.60595 assigned negative charge : -493.1471 centred at (gu) : 90.94340 92.39011 86.08526 start vw surface at 0.1400000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 206705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28105 grid for indexing accessible points = 1.400000 m= 108641 mr = 152965 m= 39629 mr = 89880 m= 8874 mr = 32326 m= 928 mr = 6608 m= 35 mr = 528 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 1203 time to turn everything in is 1.890000 number of dielectric boundary points 82505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 25288 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) : 1.810384 object centre at (A) : 26.98450 30.35350 6.684999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5407848 0.2112734 midg,1,midg; midg,igrid,midg 0.1118276 -8.7783940E-02 1,midg,midg; igrid,midg,midg 0.3664478 0.1497395 gauss-seidel spectral radius is 0.9992563 estimated iterations to convergence 289 setup time was (sec) 2.240000 now iterating at: 07:38:33 rms-change max change #iterations 10.64579 272.2120 at 10iterations 6.253837 121.7491 at 20iterations 3.636754 69.89487 at 30iterations 2.114668 37.39990 at 40iterations 1.221140 21.99287 at 50iterations 0.7047455 13.78375 at 60iterations 0.4061893 7.338875 at 70iterations 0.2340048 3.987347 at 80iterations 0.1348910 2.288319 at 90iterations 7.7330366E-02 1.332659 at 100iterations 4.4428889E-02 0.7744513 at 110iterations 2.5563899E-02 0.4413528 at 120iterations 1.4705355E-02 0.2537909 at 130iterations 8.4803347E-03 0.1479841 at 140iterations 4.8971865E-03 9.4161987E-02 at 150iterations 2.8526774E-03 5.0552368E-02 at 160iterations 1.6856827E-03 2.8823853E-02 at 170iterations 1.0176342E-03 1.9417763E-02 at 180iterations finished qdiffx linear iterations at : 07:38:50 total time elapsed so far: 18.61000 # loops : 180 mean,max change (kT/e) : 1.0176342E-03 1.9417763E-02 energy calculations done at 18.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.78000 DelPhi exited at 07:38:50 18.784u 0.465s 0:19.71 97.6% 0+0k 0+0io 0pf+0w