Sun Nov 13 16:11:24 PST 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 Sun Nov 13 2011 at 16:11:24 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 ! Automatically converted by prot2crg.py # of charge parameter records: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2571 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6082455 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): -5.624000 46.76500 ymin,ymax (A): 16.33800 67.79000 zmin,zma (A): 62.73400 121.2630 x,y,z range (A): 52.38900 51.45200 58.52900 scale (grids/A): 0.6082455 object centre (A): 20.57050 42.06400 91.99850 number of atom coordinates read : 2571 total number of charged atoms : 2431 net assigned charge : 6.000024 assigned positive charge : 374.9931 centred at (gu) : 88.80467 89.82468 89.55476 assigned negative charge : -368.9936 centred at (gu) : 88.76483 89.91130 89.47994 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6479 nv = 96 ne = 84 npr = 51498 no. pairs analyzed = 51498 no. exposed pairs = 3343 no. arc points = 23982 no. surface atoms = 1117 nbur = 1454 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 305 mr = 3307 m= 3 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2457 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7962 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0467851E-13 6.0590319E-09 midg,1,midg; midg,igrid,midg 7.4925381E-09 -4.9055593E-10 1,midg,midg; igrid,midg,midg 2.0413253E-09 3.9626369E-09 gauss-seidel spectral radius is 0.9860139 estimated iterations to convergence 69 setup time was (sec) 0.4300000 now iterating at: 16:11:25 rms-change max change #iterations 0.1124112 18.00368 at 10iterations 9.9502336E-03 1.981630 at 20iterations 8.7557163E-04 0.1440277 at 30iterations 7.7203629E-05 1.1100769E-02 at 40iterations 6.9272451E-06 1.0108948E-03 at 50iterations finished qdiffx linear iterations at : 16:11:28 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 6.9272451E-06 1.0108948E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 16:11:28 3.532u 0.187s 0:04.05 91.6% 0+0k 1896+45816io 3pf+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 Nov 13 2011 at 16:11:28 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 ! Automatically converted by prot2crg.py # of charge parameter records: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2571 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.824736 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): -5.624000 46.76500 ymin,ymax (A): 16.33800 67.79000 zmin,zma (A): 62.73400 121.2630 x,y,z range (A): 52.38900 51.45200 58.52900 scale (grids/A): 1.824736 object centre (A): 20.57050 42.06400 91.99850 number of atom coordinates read : 2571 total number of charged atoms : 2431 net assigned charge : 6.000024 assigned positive charge : 374.9931 centred at (gu) : 86.41348 89.47372 88.66380 assigned negative charge : -368.9936 centred at (gu) : 86.29404 89.73376 88.43964 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 70264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23982 grid for indexing accessible points = 1.400000 m= 24307 mr = 47160 m= 3418 mr = 17190 m= 175 mr = 1796 m= 0 mr = 47 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 31971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 19019 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) : 0.6082455 object centre at (A) : 20.57050 42.06400 91.99850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8530300E-02 1.3061495E-02 midg,1,midg; midg,igrid,midg 3.3637535E-02 1.4136317E-03 1,midg,midg; igrid,midg,midg -1.4604868E-02 1.5187233E-02 gauss-seidel spectral radius is 0.9985265 estimated iterations to convergence 207 setup time was (sec) 0.6500000 now iterating at: 16:11:29 rms-change max change #iterations 3.812099 170.8693 at 10iterations 1.732697 65.76148 at 20iterations 0.7841804 25.20310 at 30iterations 0.3564620 11.80336 at 40iterations 0.1612237 5.746628 at 50iterations 7.3328063E-02 2.576977 at 60iterations 3.3343457E-02 1.053151 at 70iterations 1.5070750E-02 0.5741043 at 80iterations 6.8823989E-03 0.2318625 at 90iterations 3.1173602E-03 0.1045685 at 100iterations 1.4139229E-03 4.5966506E-02 at 110iterations 6.4352399E-04 2.0973682E-02 at 120iterations finished qdiffx linear iterations at : 16:11:36 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 6.4352399E-04 2.0973682E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 16:11:37 8.052u 0.205s 0:08.56 96.3% 0+0k 0+45240io 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 Nov 13 2011 at 16:11:37 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 ! Automatically converted by prot2crg.py # of charge parameter records: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2571 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.737105 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): -5.624000 46.76500 ymin,ymax (A): 16.33800 67.79000 zmin,zma (A): 62.73400 121.2630 x,y,z range (A): 52.38900 51.45200 58.52900 scale (grids/A): 2.737105 object centre (A): 20.57050 42.06400 91.99850 number of atom coordinates read : 2571 total number of charged atoms : 2431 net assigned charge : 6.000024 assigned positive charge : 374.9931 centred at (gu) : 84.62014 89.21040 87.99563 assigned negative charge : -368.9936 centred at (gu) : 84.44102 89.60052 87.65939 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 162526 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23982 grid for indexing accessible points = 1.400000 m= 79226 mr = 114960 m= 27121 mr = 63049 m= 5675 mr = 20918 m= 721 mr = 3821 m= 21 mr = 416 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.130000 number of dielectric boundary points 72124 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 19439 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) : 1.824736 object centre at (A) : 20.57050 42.06400 91.99850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4811056 4.1290127E-02 midg,1,midg; midg,igrid,midg 0.3289662 -2.3375914E-02 1,midg,midg; igrid,midg,midg -0.2747539 0.1508973 gauss-seidel spectral radius is 0.9992359 estimated iterations to convergence 286 setup time was (sec) 1.360000 now iterating at: 16:11:38 rms-change max change #iterations 9.286083 327.1578 at 10iterations 5.448631 138.9764 at 20iterations 3.156597 76.03738 at 30iterations 1.820961 42.01629 at 40iterations 1.048733 21.05762 at 50iterations 0.6006337 13.38804 at 60iterations 0.3441347 7.234592 at 70iterations 0.1968344 4.151821 at 80iterations 0.1124260 2.256063 at 90iterations 6.4068004E-02 1.236504 at 100iterations 3.6614824E-02 0.7571831 at 110iterations 2.0832181E-02 0.4050379 at 120iterations 1.1879163E-02 0.2332096 at 130iterations 6.7590023E-03 0.1380615 at 140iterations 3.8475723E-03 7.6165676E-02 at 150iterations 2.1897922E-03 5.0836563E-02 at 160iterations 1.2494298E-03 2.4190903E-02 at 170iterations 7.1252492E-04 1.3677120E-02 at 180iterations finished qdiffx linear iterations at : 16:11:50 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 7.1252492E-04 1.3677120E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 16:11:50 12.936u 0.234s 0:13.45 97.8% 0+0k 0+45232io 0pf+0w