Sat Oct 8 16:05:07 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 Sat Oct 8 2011 at 16:05:07 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 = 2300 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6537628 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): -2.001000 45.77700 ymin,ymax (A): -16.58900 29.21400 zmin,zma (A): -17.77800 36.67600 x,y,z range (A): 47.77800 45.80300 54.45400 scale (grids/A): 0.6537628 object centre (A): 21.88800 6.312499 9.448999 number of atom coordinates read : 2300 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 90.54980 88.90022 90.24658 assigned negative charge : -338.3788 centred at (gu) : 90.60179 89.04115 90.29216 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6664 nv = 96 ne = 84 npr = 46214 no. pairs analyzed = 46214 no. exposed pairs = 2969 no. arc points = 20289 no. surface atoms = 1001 nbur = 1299 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 3665 m= 1 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.3200000 number of dielectric boundary points 3338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1956 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7966 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4297618E-08 1.7412664E-09 midg,1,midg; midg,igrid,midg 3.6308062E-08 -9.8728572E-09 1,midg,midg; igrid,midg,midg 1.4258511E-08 7.5344553E-10 gauss-seidel spectral radius is 0.9878507 estimated iterations to convergence 74 setup time was (sec) 0.5800000 now iterating at: 16:05:07 rms-change max change #iterations 0.1489204 21.07736 at 10iterations 1.5341564E-02 2.286758 at 20iterations 1.6506771E-03 0.2450466 at 30iterations 1.8949932E-04 2.9384613E-02 at 40iterations 2.9360601E-05 4.6641827E-03 at 50iterations finished qdiffx linear iterations at : 16:05:11 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 2.9360601E-05 4.6641827E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 16:05:11 4.090u 0.281s 0:04.67 93.5% 0+0k 0+0io 6pf+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 Sat Oct 8 2011 at 16:05:11 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 = 2300 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.961288 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): -2.001000 45.77700 ymin,ymax (A): -16.58900 29.21400 zmin,zma (A): -17.77800 36.67600 x,y,z range (A): 47.77800 45.80300 54.45400 scale (grids/A): 1.961288 object centre (A): 21.88800 6.312499 9.448999 number of atom coordinates read : 2300 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 91.64895 86.70046 90.73930 assigned negative charge : -338.3788 centred at (gu) : 91.80529 87.12348 90.87630 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 71475 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20289 grid for indexing accessible points = 1.400000 m= 26632 mr = 49382 m= 4853 mr = 19795 m= 328 mr = 3303 m= 7 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 914 time to turn everything in is 0.6400000 number of dielectric boundary points 30671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 17582 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) : 0.6537628 object centre at (A) : 21.88800 6.312499 9.448999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3226932E-02 -1.6751517E-02 midg,1,midg; midg,igrid,midg 3.1388965E-02 -5.1663974E-03 1,midg,midg; igrid,midg,midg 5.8319643E-03 -3.7523534E-02 gauss-seidel spectral radius is 0.9986836 estimated iterations to convergence 218 setup time was (sec) 0.9500000 now iterating at: 16:05:13 rms-change max change #iterations 4.184375 181.7339 at 10iterations 1.985840 68.47449 at 20iterations 0.9420033 33.02794 at 30iterations 0.4501732 15.85388 at 40iterations 0.2131194 6.453379 at 50iterations 0.1015655 3.404280 at 60iterations 4.8233636E-02 1.558435 at 70iterations 2.2909706E-02 0.7451591 at 80iterations 1.0907190E-02 0.3466039 at 90iterations 5.2084220E-03 0.1648202 at 100iterations 2.4749089E-03 7.7884674E-02 at 110iterations 1.1801515E-03 3.8188934E-02 at 120iterations finished qdiffx linear iterations at : 16:05:21 total time elapsed so far: 9.380000 # loops : 120 mean,max change (kT/e) : 1.1801515E-03 3.8188934E-02 energy calculations done at 9.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.560000 DelPhi exited at 16:05:22 9.560u 0.312s 0:10.16 97.1% 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 Sat Oct 8 2011 at 16:05:22 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 = 2300 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.941933 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): -2.001000 45.77700 ymin,ymax (A): -16.58900 29.21400 zmin,zma (A): -17.77800 36.67600 x,y,z range (A): 47.77800 45.80300 54.45400 scale (grids/A): 2.941933 object centre (A): 21.88800 6.312499 9.448999 number of atom coordinates read : 2300 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 92.47327 85.05052 91.10887 assigned negative charge : -338.3788 centred at (gu) : 92.70785 85.68521 91.31447 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 165285 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20289 grid for indexing accessible points = 1.400000 m= 84173 mr = 119819 m= 32733 mr = 68928 m= 9104 mr = 26720 m= 1466 mr = 7196 m= 120 mr = 1059 m= 5 mr = 57 m= 0 mr = 2 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 3192 time to turn everything in is 1.670000 number of dielectric boundary points 69105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 17839 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) : 1.961288 object centre at (A) : 21.88800 6.312499 9.448999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2255443 -0.2425946 midg,1,midg; midg,igrid,midg 0.2608138 -7.4019894E-02 1,midg,midg; igrid,midg,midg 4.7838300E-02 -0.5217910 gauss-seidel spectral radius is 0.9992712 estimated iterations to convergence 292 setup time was (sec) 2.000000 now iterating at: 16:05:24 rms-change max change #iterations 9.695010 428.4939 at 10iterations 5.666365 122.4573 at 20iterations 3.309141 80.51311 at 30iterations 1.932138 42.48429 at 40iterations 1.125077 20.67878 at 50iterations 0.6559821 13.16926 at 60iterations 0.3795777 7.706388 at 70iterations 0.2199733 3.947807 at 80iterations 0.1275298 2.412742 at 90iterations 7.3819607E-02 1.407990 at 100iterations 4.2814977E-02 0.7722069 at 110iterations 2.4683122E-02 0.4821607 at 120iterations 1.4273802E-02 0.2573051 at 130iterations 8.2572959E-03 0.1676655 at 140iterations 4.7639669E-03 8.7753296E-02 at 150iterations 2.7578480E-03 4.7089577E-02 at 160iterations 1.5916589E-03 3.0766010E-02 at 170iterations 9.2167582E-04 1.5966415E-02 at 180iterations finished qdiffx linear iterations at : 16:05:38 total time elapsed so far: 16.10000 # loops : 180 mean,max change (kT/e) : 9.2167582E-04 1.5966415E-02 energy calculations done at 16.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.27000 DelPhi exited at 16:05:38 16.275u 0.340s 0:16.90 98.2% 0+0k 0+0io 0pf+0w