Mon Oct 10 00:41:33 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 Mon Oct 10 2011 at 00:41:33 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2210 !!! WARNING: HIR 127 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: 0.6870332 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): -9.566000 42.25100 ymin,ymax (A): -52.47000 -3.719000 zmin,zma (A): -23.75600 24.34100 x,y,z range (A): 51.81700 48.75100 48.09700 scale (grids/A): 0.6870332 object centre (A): 16.34250 -28.09450 0.2924995 number of atom coordinates read : 2210 total number of charged atoms : 2068 net assigned charge : 5.014013 assigned positive charge : 331.1115 centred at (gu) : 88.60891 89.03700 90.25921 assigned negative charge : -326.0978 centred at (gu) : 88.48293 89.03744 90.25307 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7260 nv = 96 ne = 84 npr = 43914 no. pairs analyzed = 43914 no. exposed pairs = 3070 no. arc points = 21264 no. surface atoms = 1036 nbur = 1174 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 426 mr = 3741 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1892 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8025 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3171614E-08 2.9779470E-08 midg,1,midg; midg,igrid,midg 3.1933816E-08 2.1769669E-08 1,midg,midg; igrid,midg,midg -2.0328091E-08 5.0398526E-08 gauss-seidel spectral radius is 0.9889880 estimated iterations to convergence 78 setup time was (sec) 0.3600000 now iterating at: 00:41:34 rms-change max change #iterations 0.1885942 29.85979 at 10iterations 2.1639690E-02 3.127652 at 20iterations 2.4638667E-03 0.3661385 at 30iterations 2.8432108E-04 3.6016464E-02 at 40iterations 3.3713233E-05 4.6920776E-03 at 50iterations finished qdiffx linear iterations at : 00:41:37 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 3.3713233E-05 4.6920776E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 00:41:37 3.379u 0.182s 0:03.88 91.4% 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 Mon Oct 10 2011 at 00:41:37 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2210 !!! WARNING: HIR 127 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: 2.061100 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): -9.566000 42.25100 ymin,ymax (A): -52.47000 -3.719000 zmin,zma (A): -23.75600 24.34100 x,y,z range (A): 51.81700 48.75100 48.09700 scale (grids/A): 2.061100 object centre (A): 16.34250 -28.09450 0.2924995 number of atom coordinates read : 2210 total number of charged atoms : 2068 net assigned charge : 5.014013 assigned positive charge : 331.1115 centred at (gu) : 85.82640 87.11064 90.77721 assigned negative charge : -326.0978 centred at (gu) : 85.44883 87.11210 90.75901 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76698 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21264 grid for indexing accessible points = 1.400000 m= 28232 mr = 51357 m= 5531 mr = 20136 m= 505 mr = 3558 m= 18 mr = 257 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 35674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 16400 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) : 0.6870332 object centre at (A) : 16.34250 -28.09450 0.2924995 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4872971E-02 2.8492821E-02 midg,1,midg; midg,igrid,midg 1.0927987E-02 -2.2573994E-02 1,midg,midg; igrid,midg,midg 1.7346967E-02 3.1745501E-02 gauss-seidel spectral radius is 0.9988050 estimated iterations to convergence 229 setup time was (sec) 0.6000000 now iterating at: 00:41:38 rms-change max change #iterations 4.556977 184.4529 at 10iterations 2.223554 76.81499 at 20iterations 1.095934 36.25325 at 30iterations 0.5388057 15.56056 at 40iterations 0.2643344 7.860214 at 50iterations 0.1298249 4.179581 at 60iterations 6.3766815E-02 1.922394 at 70iterations 3.1338755E-02 0.9249668 at 80iterations 1.5422085E-02 0.4966087 at 90iterations 7.5763315E-03 0.2463474 at 100iterations 3.7257506E-03 0.1145573 at 110iterations 1.8326548E-03 6.3148499E-02 at 120iterations finished qdiffx linear iterations at : 00:41:45 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 1.8326548E-03 6.3148499E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 00:41:46 7.907u 0.203s 0:08.44 95.9% 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 Mon Oct 10 2011 at 00:41:46 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2210 !!! WARNING: HIR 127 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: 3.091649 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): -9.566000 42.25100 ymin,ymax (A): -52.47000 -3.719000 zmin,zma (A): -23.75600 24.34100 x,y,z range (A): 51.81700 48.75100 48.09700 scale (grids/A): 3.091649 object centre (A): 16.34250 -28.09450 0.2924995 number of atom coordinates read : 2210 total number of charged atoms : 2068 net assigned charge : 5.014013 assigned positive charge : 331.1115 centred at (gu) : 83.73956 85.66601 91.16587 assigned negative charge : -326.0978 centred at (gu) : 83.17316 85.66808 91.13851 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 177229 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21264 grid for indexing accessible points = 1.400000 m= 88260 mr = 125218 m= 35071 mr = 70311 m= 10207 mr = 27767 m= 2058 mr = 7731 m= 253 mr = 1478 m= 14 mr = 180 m= 0 mr = 4 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.170000 number of dielectric boundary points 80403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 16544 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) : 2.061100 object centre at (A) : 16.34250 -28.09450 0.2924995 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7604637 0.2219244 midg,1,midg; midg,igrid,midg 5.3884156E-02 -0.3813342 1,midg,midg; igrid,midg,midg 0.2643866 0.2593660 gauss-seidel spectral radius is 0.9993074 estimated iterations to convergence 300 setup time was (sec) 1.410000 now iterating at: 00:41:47 rms-change max change #iterations 10.35172 469.6136 at 10iterations 6.169611 126.9737 at 20iterations 3.662492 78.74226 at 30iterations 2.170582 40.60286 at 40iterations 1.281611 22.24319 at 50iterations 0.7565987 13.34594 at 60iterations 0.4448135 8.297165 at 70iterations 0.2609463 4.936915 at 80iterations 0.1535905 2.872700 at 90iterations 9.0038739E-02 1.646454 at 100iterations 5.2882604E-02 0.9118371 at 110iterations 3.0962897E-02 0.5511026 at 120iterations 1.8159576E-02 0.3162994 at 130iterations 1.0622204E-02 0.1935692 at 140iterations 6.2255869E-03 0.1286430 at 150iterations 3.6413644E-03 6.4968109E-02 at 160iterations 2.1365706E-03 3.5770416E-02 at 170iterations 1.2508321E-03 2.2113800E-02 at 180iterations finished qdiffx linear iterations at : 00:41:59 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 1.2508321E-03 2.2113800E-02 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.02000 DelPhi exited at 00:41:59 13.025u 0.214s 0:13.51 97.9% 0+0k 0+0io 0pf+0w