Sun Oct 9 22:49:43 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 Sun Oct 9 2011 at 22:49:44 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 = 2177 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: 0.6329902 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): 0.9620000 50.33900 ymin,ymax (A): 0.9350001 57.17600 zmin,zma (A): -6.809000 33.53100 x,y,z range (A): 49.37700 56.24100 40.34000 scale (grids/A): 0.6329902 object centre (A): 25.65050 29.05550 13.36100 number of atom coordinates read : 2177 total number of charged atoms : 2038 net assigned charge : 3.500001 assigned positive charge : 322.8965 centred at (gu) : 88.87959 90.38976 90.44833 assigned negative charge : -319.3969 centred at (gu) : 89.04046 90.52641 90.31789 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5977 nv = 96 ne = 84 npr = 42665 no. pairs analyzed = 42665 no. exposed pairs = 2850 no. arc points = 20031 no. surface atoms = 964 nbur = 1213 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3178 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.2600000 number of dielectric boundary points 3110 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1906 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7038 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8245444E-09 1.5634290E-08 midg,1,midg; midg,igrid,midg 1.3471956E-08 -7.6035480E-09 1,midg,midg; igrid,midg,midg 2.1101750E-08 -6.9467188E-09 gauss-seidel spectral radius is 0.9870387 estimated iterations to convergence 72 setup time was (sec) 0.5500000 now iterating at: 22:49:44 rms-change max change #iterations 0.1252246 19.55853 at 10iterations 1.2113920E-02 1.965965 at 20iterations 1.2497132E-03 0.2002940 at 30iterations 2.2821366E-04 4.4797897E-02 at 40iterations 8.8286099E-05 1.8837929E-02 at 50iterations finished qdiffx linear iterations at : 22:49:48 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 8.8286099E-05 1.8837929E-02 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 22:49:49 4.267u 0.290s 0:05.02 90.6% 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 Sun Oct 9 2011 at 22:49:49 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 = 2177 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: 1.898970 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): 0.9620000 50.33900 ymin,ymax (A): 0.9350001 57.17600 zmin,zma (A): -6.809000 33.53100 x,y,z range (A): 49.37700 56.24100 40.34000 scale (grids/A): 1.898970 object centre (A): 25.65050 29.05550 13.36100 number of atom coordinates read : 2177 total number of charged atoms : 2038 net assigned charge : 3.500001 assigned positive charge : 322.8965 centred at (gu) : 86.63831 91.16911 91.34458 assigned negative charge : -319.3969 centred at (gu) : 87.12143 91.57912 90.95359 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 64453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20031 grid for indexing accessible points = 1.400000 m= 21862 mr = 43694 m= 3236 mr = 15625 m= 197 mr = 1893 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 304 time to turn everything in is 0.5800000 number of dielectric boundary points 28473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 16020 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) : 0.6329902 object centre at (A) : 25.65050 29.05550 13.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6229672E-03 1.3301366E-02 midg,1,midg; midg,igrid,midg -7.1297102E-03 -8.3823521E-03 1,midg,midg; igrid,midg,midg 3.7778012E-02 1.4860309E-02 gauss-seidel spectral radius is 0.9985892 estimated iterations to convergence 211 setup time was (sec) 0.9500000 now iterating at: 22:49:50 rms-change max change #iterations 3.760009 164.3603 at 10iterations 1.746104 64.05450 at 20iterations 0.8081045 27.64363 at 30iterations 0.3748232 12.67814 at 40iterations 0.1739322 6.459696 at 50iterations 8.0351807E-02 2.695370 at 60iterations 3.7242796E-02 1.315939 at 70iterations 1.7303266E-02 0.5962868 at 80iterations 8.0084261E-03 0.2770709 at 90iterations 3.7200914E-03 0.1212463 at 100iterations 1.7257148E-03 5.6923866E-02 at 110iterations 8.1033399E-04 2.8093338E-02 at 120iterations finished qdiffx linear iterations at : 22:49:59 total time elapsed so far: 9.730000 # loops : 120 mean,max change (kT/e) : 8.1033399E-04 2.8093338E-02 energy calculations done at 9.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.910000 DelPhi exited at 22:49:59 9.912u 0.337s 0:10.71 95.6% 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 Sun Oct 9 2011 at 22:49:59 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 = 2177 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: 2.848456 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): 0.9620000 50.33900 ymin,ymax (A): 0.9350001 57.17600 zmin,zma (A): -6.809000 33.53100 x,y,z range (A): 49.37700 56.24100 40.34000 scale (grids/A): 2.848456 object centre (A): 25.65050 29.05550 13.36100 number of atom coordinates read : 2177 total number of charged atoms : 2038 net assigned charge : 3.500001 assigned positive charge : 322.8965 centred at (gu) : 84.95738 91.75360 92.01692 assigned negative charge : -319.3969 centred at (gu) : 85.68216 92.36874 91.43036 start vw surface at 0.1400000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 149249 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20031 grid for indexing accessible points = 1.400000 m= 72483 mr = 106521 m= 24539 mr = 58201 m= 5639 mr = 19162 m= 795 mr = 4076 m= 33 mr = 521 m= 0 mr = 11 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 1056 time to turn everything in is 1.370000 number of dielectric boundary points 64246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 16304 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) : 1.898970 object centre at (A) : 25.65050 29.05550 13.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8507464E-03 0.1198525 midg,1,midg; midg,igrid,midg -0.2126382 6.5879770E-02 1,midg,midg; igrid,midg,midg 0.4183944 0.2344041 gauss-seidel spectral radius is 0.9992440 estimated iterations to convergence 287 setup time was (sec) 1.710000 now iterating at: 22:50:01 rms-change max change #iterations 9.002271 333.7561 at 10iterations 5.266531 137.2207 at 20iterations 3.052596 65.49982 at 30iterations 1.764714 37.63648 at 40iterations 1.017296 23.43472 at 50iterations 0.5853632 12.29491 at 60iterations 0.3354981 7.333617 at 70iterations 0.1922528 3.859488 at 80iterations 0.1105341 2.449275 at 90iterations 6.3245170E-02 1.343870 at 100iterations 3.6218815E-02 0.7718124 at 110iterations 2.0729087E-02 0.4658699 at 120iterations 1.1859466E-02 0.2423325 at 130iterations 6.7804051E-03 0.1418886 at 140iterations 3.8755627E-03 7.6370716E-02 at 150iterations 2.2191836E-03 4.4401169E-02 at 160iterations 1.2700206E-03 2.7565002E-02 at 170iterations 7.3292764E-04 1.4769554E-02 at 180iterations finished qdiffx linear iterations at : 22:50:15 total time elapsed so far: 15.76000 # loops : 180 mean,max change (kT/e) : 7.3292764E-04 1.4769554E-02 energy calculations done at 15.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.95000 DelPhi exited at 22:50:16 15.948u 0.364s 0:16.64 97.9% 0+0k 0+0io 0pf+0w