Wed Dec 28 11:01:19 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 Wed Dec 28 2011 at 11:01:19 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 0.6383704 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): -5.822000 35.46600 ymin,ymax (A): -3.677000 49.12100 zmin,zma (A): -24.52100 31.24600 x,y,z range (A): 41.28800 52.79800 55.76700 scale (grids/A): 0.6383704 object centre (A): 14.82200 22.72200 3.362500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 90.78573 92.49285 90.21811 assigned negative charge : -284.4403 centred at (gu) : 90.93972 92.63747 90.14051 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5642 nv = 96 ne = 84 npr = 39363 no. pairs analyzed = 39363 no. exposed pairs = 2524 no. arc points = 17801 no. surface atoms = 855 nbur = 1111 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 3146 m= 0 mr = 58 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1757 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6468 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1911164E-09 1.1858485E-08 midg,1,midg; midg,igrid,midg 9.7949835E-09 -1.2130918E-08 1,midg,midg; igrid,midg,midg 1.4663825E-08 -9.1006020E-09 gauss-seidel spectral radius is 0.9872355 estimated iterations to convergence 72 setup time was (sec) 0.5700000 now iterating at: 11:01:20 rms-change max change #iterations 0.1235837 21.21225 at 10iterations 1.1959971E-02 1.885380 at 20iterations 1.1816245E-03 0.2028656 at 30iterations 1.1321987E-04 1.5308380E-02 at 40iterations 1.1167968E-05 1.8243790E-03 at 50iterations finished qdiffx linear iterations at : 11:01:24 total time elapsed so far: 4.710000 # loops : 50 mean,max change (kT/e) : 1.1167968E-05 1.8243790E-03 energy calculations done at 4.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.920000 DelPhi exited at 11:01:25 4.920u 0.275s 0:05.84 88.8% 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 Wed Dec 28 2011 at 11:01:25 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 1.915111 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): -5.822000 35.46600 ymin,ymax (A): -3.677000 49.12100 zmin,zma (A): -24.52100 31.24600 x,y,z range (A): 41.28800 52.79800 55.76700 scale (grids/A): 1.915111 object centre (A): 14.82200 22.72200 3.362500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 92.35729 97.47872 90.65474 assigned negative charge : -284.4403 centred at (gu) : 92.81946 97.91258 90.42178 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 60208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17801 grid for indexing accessible points = 1.400000 m= 23468 mr = 41354 m= 4177 mr = 18248 m= 252 mr = 3017 m= 1 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1297 time to turn everything in is 0.5600000 number of dielectric boundary points 25387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 14453 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) : 0.6383704 object centre at (A) : 14.82200 22.72200 3.362500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2701766E-02 1.4197408E-02 midg,1,midg; midg,igrid,midg 3.0103121E-02 -9.9640964E-03 1,midg,midg; igrid,midg,midg 8.7285172E-03 -4.3859538E-03 gauss-seidel spectral radius is 0.9985772 estimated iterations to convergence 210 setup time was (sec) 0.8800000 now iterating at: 11:01:26 rms-change max change #iterations 3.572818 177.7747 at 10iterations 1.649249 66.66286 at 20iterations 0.7618196 29.12928 at 30iterations 0.3517521 13.15250 at 40iterations 0.1618188 6.229257 at 50iterations 7.4454851E-02 2.541862 at 60iterations 3.4330938E-02 1.176763 at 70iterations 1.5765827E-02 0.5230274 at 80iterations 7.2944206E-03 0.2727585 at 90iterations 3.3651986E-03 0.1158333 at 100iterations 1.5510496E-03 5.1910400E-02 at 110iterations 7.1165373E-04 2.5561690E-02 at 120iterations finished qdiffx linear iterations at : 11:01:37 total time elapsed so far: 11.68000 # loops : 120 mean,max change (kT/e) : 7.1165373E-04 2.5561690E-02 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.87000 DelPhi exited at 11:01:38 11.876u 0.437s 0:13.28 92.6% 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 Wed Dec 28 2011 at 11:01:38 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 2.872667 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): -5.822000 35.46600 ymin,ymax (A): -3.677000 49.12100 zmin,zma (A): -24.52100 31.24600 x,y,z range (A): 41.28800 52.79800 55.76700 scale (grids/A): 2.872667 object centre (A): 14.82200 22.72200 3.362500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 93.53593 101.2183 90.98203 assigned negative charge : -284.4403 centred at (gu) : 94.22920 101.8690 90.63271 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 138792 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17801 grid for indexing accessible points = 1.400000 m= 73592 mr = 99664 m= 29485 mr = 61666 m= 7780 mr = 24964 m= 1153 mr = 6413 m= 70 mr = 853 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 4659 time to turn everything in is 1.410000 number of dielectric boundary points 57272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 14656 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) : 1.915111 object centre at (A) : 14.82200 22.72200 3.362500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.065471 1.1801166E-02 midg,1,midg; midg,igrid,midg 0.2860135 -0.1191819 1,midg,midg; igrid,midg,midg 4.9463890E-02 -1.6639758E-02 gauss-seidel spectral radius is 0.9992310 estimated iterations to convergence 285 setup time was (sec) 1.770000 now iterating at: 11:01:41 rms-change max change #iterations 8.446002 423.5996 at 10iterations 4.850760 134.1432 at 20iterations 2.756808 71.96590 at 30iterations 1.571877 31.61343 at 40iterations 0.8934054 20.89099 at 50iterations 0.5078866 11.28398 at 60iterations 0.2883534 6.767749 at 70iterations 0.1634313 3.272031 at 80iterations 9.2691459E-02 1.836784 at 90iterations 5.2642979E-02 1.197346 at 100iterations 2.9799404E-02 0.6284409 at 110iterations 1.6968125E-02 0.3290482 at 120iterations 9.5974542E-03 0.1856251 at 130iterations 5.4442855E-03 0.1074696 at 140iterations 3.0863069E-03 5.8389485E-02 at 150iterations 1.7540780E-03 3.3850193E-02 at 160iterations 9.9567790E-04 1.9566059E-02 at 170iterations 5.6369836E-04 1.1207581E-02 at 180iterations finished qdiffx linear iterations at : 11:01:59 total time elapsed so far: 19.89000 # loops : 180 mean,max change (kT/e) : 5.6369836E-04 1.1207581E-02 energy calculations done at 19.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.08000 DelPhi exited at 11:01:59 20.080u 0.377s 0:21.06 97.1% 0+0k 0+0io 0pf+0w