Sun Oct 9 10:23:56 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 10:23:56 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 # of charge parameter records: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2191 !!! WARNING: HIR 524 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6712295 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): -1.550000 48.52400 ymin,ymax (A): -26.63700 26.40000 zmin,zma (A): -4.092000 48.34900 x,y,z range (A): 50.07400 53.03700 52.44100 scale (grids/A): 0.6712295 object centre (A): 23.48700 -0.1184998 22.12850 number of atom coordinates read : 2191 total number of charged atoms : 2054 net assigned charge : 1.514015 assigned positive charge : 319.6907 centred at (gu) : 90.66047 92.29514 90.69881 assigned negative charge : -318.1773 centred at (gu) : 90.69949 92.15391 90.63830 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6892 nv = 96 ne = 84 npr = 43757 no. pairs analyzed = 43757 no. exposed pairs = 2946 no. arc points = 20831 no. surface atoms = 977 nbur = 1214 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 434 mr = 3632 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.1700000 number of dielectric boundary points 3626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1908 ## 147 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7721 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.4545445E-09 1.9908269E-08 midg,1,midg; midg,igrid,midg -1.6292269E-08 5.5334006E-08 1,midg,midg; igrid,midg,midg 1.1087541E-08 -4.6653077E-09 gauss-seidel spectral radius is 0.9884676 estimated iterations to convergence 76 setup time was (sec) 0.3800000 now iterating at: 10:23:57 rms-change max change #iterations 0.1615454 23.81411 at 10iterations 1.7995242E-02 2.698452 at 20iterations 1.9659549E-03 0.2616720 at 30iterations 2.1505202E-04 3.9002180E-02 at 40iterations 2.3550858E-05 3.3645630E-03 at 50iterations finished qdiffx linear iterations at : 10:24:00 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 2.3550858E-05 3.3645630E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 10:24:00 3.558u 0.218s 0:04.05 92.8% 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 Sun Oct 9 2011 at 10:24:00 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2191 !!! WARNING: HIR 524 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.013689 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): -1.550000 48.52400 ymin,ymax (A): -26.63700 26.40000 zmin,zma (A): -4.092000 48.34900 x,y,z range (A): 50.07400 53.03700 52.44100 scale (grids/A): 2.013689 object centre (A): 23.48700 -0.1184998 22.12850 number of atom coordinates read : 2191 total number of charged atoms : 2054 net assigned charge : 1.514015 assigned positive charge : 319.6907 centred at (gu) : 91.98126 96.88499 92.09610 assigned negative charge : -318.1773 centred at (gu) : 92.09865 96.46191 91.91513 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73350 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20831 grid for indexing accessible points = 1.400000 m= 27047 mr = 49298 m= 4955 mr = 19792 m= 426 mr = 3330 m= 2 mr = 213 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 738 time to turn everything in is 0.3800000 number of dielectric boundary points 33147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 16254 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) : 0.6712295 object centre at (A) : 23.48700 -0.1184998 22.12850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1653717E-02 5.0006751E-02 midg,1,midg; midg,igrid,midg -4.3357224E-03 6.4191043E-02 1,midg,midg; igrid,midg,midg -1.8281346E-02 -2.8571494E-02 gauss-seidel spectral radius is 0.9987410 estimated iterations to convergence 223 setup time was (sec) 0.6200000 now iterating at: 10:24:01 rms-change max change #iterations 4.287267 214.5237 at 10iterations 2.061176 81.90520 at 20iterations 1.001629 34.93465 at 30iterations 0.4825129 15.98611 at 40iterations 0.2336373 7.609536 at 50iterations 0.1129351 3.836832 at 60iterations 5.4526929E-02 1.744462 at 70iterations 2.6344961E-02 0.7884521 at 80iterations 1.2697644E-02 0.4042358 at 90iterations 6.1330548E-03 0.1957550 at 100iterations 2.9691197E-03 9.3952179E-02 at 110iterations 1.4344217E-03 4.8446655E-02 at 120iterations finished qdiffx linear iterations at : 10:24:09 total time elapsed so far: 8.210000 # loops : 120 mean,max change (kT/e) : 1.4344217E-03 4.8446655E-02 energy calculations done at 8.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.340000 DelPhi exited at 10:24:09 8.347u 0.222s 0:08.94 95.7% 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 Sun Oct 9 2011 at 10:24:09 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2191 !!! WARNING: HIR 524 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.020533 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): -1.550000 48.52400 ymin,ymax (A): -26.63700 26.40000 zmin,zma (A): -4.092000 48.34900 x,y,z range (A): 50.07400 53.03700 52.44100 scale (grids/A): 3.020533 object centre (A): 23.48700 -0.1184998 22.12850 number of atom coordinates read : 2191 total number of charged atoms : 2054 net assigned charge : 1.514015 assigned positive charge : 319.6907 centred at (gu) : 92.97177 100.3274 93.14407 assigned negative charge : -318.1773 centred at (gu) : 93.14793 99.69299 92.87265 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 169301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20831 grid for indexing accessible points = 1.400000 m= 84545 mr = 119391 m= 33210 mr = 68621 m= 9284 mr = 26802 m= 1864 mr = 7243 m= 160 mr = 1414 m= 1 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 2497 time to turn everything in is 0.9800000 number of dielectric boundary points 74808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 16432 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) : 2.013689 object centre at (A) : 23.48700 -0.1184998 22.12850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2968487 0.6068276 midg,1,midg; midg,igrid,midg -6.3977286E-02 0.4870423 1,midg,midg; igrid,midg,midg -0.2401065 -0.3483520 gauss-seidel spectral radius is 0.9992899 estimated iterations to convergence 296 setup time was (sec) 1.240000 now iterating at: 10:24:11 rms-change max change #iterations 9.769382 462.1178 at 10iterations 5.697746 119.7414 at 20iterations 3.326211 63.44508 at 30iterations 1.947509 35.34871 at 40iterations 1.134650 21.53391 at 50iterations 0.6603711 11.76743 at 60iterations 0.3847087 6.979826 at 70iterations 0.2230695 4.567313 at 80iterations 0.1296986 2.265853 at 90iterations 7.5571492E-02 1.396974 at 100iterations 4.3824788E-02 0.7311034 at 110iterations 2.5496654E-02 0.4383937 at 120iterations 1.4780204E-02 0.2502530 at 130iterations 8.5857213E-03 0.1480637 at 140iterations 4.9858005E-03 8.4838867E-02 at 150iterations 2.8966218E-03 5.1188946E-02 at 160iterations 1.6889310E-03 3.1631470E-02 at 170iterations 9.8214275E-04 1.7311096E-02 at 180iterations finished qdiffx linear iterations at : 10:24:23 total time elapsed so far: 13.38000 # loops : 180 mean,max change (kT/e) : 9.8214275E-04 1.7311096E-02 energy calculations done at 13.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.51000 DelPhi exited at 10:24:23 13.514u 0.242s 0:14.12 97.3% 0+0k 0+0io 0pf+0w