Tue Oct 11 08:34:01 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+sph.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 = amb.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 08:34:01 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: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2097 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: 0.7047551 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): -19.70100 27.22300 ymin,ymax (A): -12.46100 28.76500 zmin,zma (A): -2.041000 48.47300 x,y,z range (A): 46.92400 41.22600 50.51400 scale (grids/A): 0.7047551 object centre (A): 3.761000 8.152000 23.21600 number of atom coordinates read : 2097 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 88.93250 89.71092 90.09722 assigned negative charge : -312.6442 centred at (gu) : 88.82253 89.73276 90.15652 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7096 nv = 96 ne = 84 npr = 42198 no. pairs analyzed = 42198 no. exposed pairs = 2543 no. arc points = 17310 no. surface atoms = 867 nbur = 1230 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4122 m= 3 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3400000 number of dielectric boundary points 3355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1574 ## 140 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7794 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8058676E-08 2.4675629E-08 midg,1,midg; midg,igrid,midg 6.5746029E-08 3.9675022E-08 1,midg,midg; igrid,midg,midg -5.3171340E-10 8.3609820E-08 gauss-seidel spectral radius is 0.9895059 estimated iterations to convergence 79 setup time was (sec) 0.6100000 now iterating at: 08:34:02 rms-change max change #iterations 0.1959819 26.24424 at 10iterations 2.4238447E-02 3.227936 at 20iterations 3.1657091E-03 0.4089470 at 30iterations 5.1258138E-04 6.4485550E-02 at 40iterations 1.2579287E-04 1.7875671E-02 at 50iterations finished qdiffx linear iterations at : 08:34:05 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 1.2579287E-04 1.7875671E-02 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 08:34:06 3.997u 0.198s 0:04.91 85.1% 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 Tue Oct 11 2011 at 08:34:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2097 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: 2.114265 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): -19.70100 27.22300 ymin,ymax (A): -12.46100 28.76500 zmin,zma (A): -2.041000 48.47300 x,y,z range (A): 46.92400 41.22600 50.51400 scale (grids/A): 2.114265 object centre (A): 3.761000 8.152000 23.21600 number of atom coordinates read : 2097 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 86.79755 89.13309 90.29194 assigned negative charge : -312.6442 centred at (gu) : 86.46764 89.19843 90.46972 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 75133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17310 grid for indexing accessible points = 1.400000 m= 30484 mr = 53784 m= 6003 mr = 23275 m= 536 mr = 4165 m= 12 mr = 298 m= 0 mr = 2 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 30644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 15610 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) : 0.7047551 object centre at (A) : 3.761000 8.152000 23.21600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8274810E-02 6.1560176E-02 midg,1,midg; midg,igrid,midg 2.7652459E-02 6.4502745E-03 1,midg,midg; igrid,midg,midg 1.8942693E-02 3.3719622E-02 gauss-seidel spectral radius is 0.9988236 estimated iterations to convergence 231 setup time was (sec) 1.070000 now iterating at: 08:34:08 rms-change max change #iterations 4.570976 234.7857 at 10iterations 2.251511 71.36833 at 20iterations 1.116248 32.95853 at 30iterations 0.5505098 17.05713 at 40iterations 0.2730337 8.738487 at 50iterations 0.1351212 4.368721 at 60iterations 6.7207336E-02 2.022676 at 70iterations 3.3273000E-02 0.9310916 at 80iterations 1.6538031E-02 0.5585232 at 90iterations 8.2628978E-03 0.2664781 at 100iterations 4.1638250E-03 0.1230087 at 110iterations 2.1231778E-03 6.3970089E-02 at 120iterations finished qdiffx linear iterations at : 08:34:15 total time elapsed so far: 8.820000 # loops : 120 mean,max change (kT/e) : 2.1231778E-03 6.3970089E-02 energy calculations done at 8.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.050000 DelPhi exited at 08:34:16 9.056u 0.163s 0:09.51 96.8% 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 08:34:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2097 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: 3.171398 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): -19.70100 27.22300 ymin,ymax (A): -12.46100 28.76500 zmin,zma (A): -2.041000 48.47300 x,y,z range (A): 46.92400 41.22600 50.51400 scale (grids/A): 3.171398 object centre (A): 3.761000 8.152000 23.21600 number of atom coordinates read : 2097 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 85.19622 88.69953 90.43774 assigned negative charge : -312.6442 centred at (gu) : 84.70152 88.79764 90.70470 start vw surface at 0.1700000 fill in re-entrant regions at 1.010000 boundary points on vw surface= 172931 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17310 grid for indexing accessible points = 1.400000 m= 94825 mr = 128717 m= 39090 mr = 79560 m= 11556 mr = 32539 m= 2431 mr = 9125 m= 237 mr = 1773 m= 5 mr = 146 m= 0 mr = 4 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.280000 number of dielectric boundary points 69211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.440000 number of grid points assigned charge 15748 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) : 2.114265 object centre at (A) : 3.761000 8.152000 23.21600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2657701 1.327045 midg,1,midg; midg,igrid,midg 0.2149405 3.2015312E-02 1,midg,midg; igrid,midg,midg 0.3229354 0.3037338 gauss-seidel spectral radius is 0.9992923 estimated iterations to convergence 297 setup time was (sec) 2.630000 now iterating at: 08:34:19 rms-change max change #iterations 10.19584 352.0524 at 10iterations 6.028122 125.6008 at 20iterations 3.544336 75.36316 at 30iterations 2.090770 41.50630 at 40iterations 1.227471 24.50381 at 50iterations 0.7201725 13.75843 at 60iterations 0.4217989 7.430061 at 70iterations 0.2468822 4.696693 at 80iterations 0.1443263 2.525539 at 90iterations 8.4307358E-02 1.590796 at 100iterations 4.9487520E-02 0.9094906 at 110iterations 2.8991621E-02 0.5833583 at 120iterations 1.7036004E-02 0.2928581 at 130iterations 1.0130003E-02 0.1851463 at 140iterations 6.0978085E-03 0.1235409 at 150iterations 3.7685323E-03 7.9553604E-02 at 160iterations 2.4160265E-03 4.3794632E-02 at 170iterations 1.6381750E-03 2.8026581E-02 at 180iterations finished qdiffx linear iterations at : 08:34:31 total time elapsed so far: 14.94000 # loops : 180 mean,max change (kT/e) : 1.6381750E-03 2.8026581E-02 energy calculations done at 14.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.18000 DelPhi exited at 08:34:32 15.182u 0.222s 0:15.88 96.9% 0+0k 0+0io 0pf+0w