Sun Oct 9 22:57:49 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+sph2.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 = amb2.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 22:57:49 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5025197 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): -21.94100 31.48900 ymin,ymax (A): -88.03900 -17.19600 zmin,zma (A): -64.11700 -0.2750000 x,y,z range (A): 53.43000 70.84300 63.84200 scale (grids/A): 0.5025197 object centre (A): 4.774000 -52.61750 -32.19600 number of atom coordinates read : 4305 total number of charged atoms : 4145 net assigned charge : 2.000011 assigned positive charge : 650.3268 centred at (gu) : 89.51080 89.14485 91.78870 assigned negative charge : -648.3315 centred at (gu) : 89.61971 89.16003 91.84225 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7116 nv = 96 ne = 84 npr = 83673 no. pairs analyzed = 83673 no. exposed pairs = 5801 no. arc points = 41189 no. surface atoms = 1928 nbur = 2377 mkacc time = 0.2800000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 247 mr = 3496 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 3858 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3967 ## 607 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 9528 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6997297E-11 -1.1305636E-10 midg,1,midg; midg,igrid,midg 5.6834766E-11 -3.7018778E-12 1,midg,midg; igrid,midg,midg 2.2517904E-10 -1.4186767E-10 gauss-seidel spectral radius is 0.9797320 estimated iterations to convergence 58 setup time was (sec) 0.8800000 now iterating at: 22:57:51 rms-change max change #iterations 5.5804275E-02 10.04144 at 10iterations 3.1126896E-03 0.5616765 at 20iterations 2.6301955E-04 6.0145378E-02 at 30iterations 6.9083646E-05 1.9013405E-02 at 40iterations 2.2745897E-05 6.2532425E-03 at 50iterations finished qdiffx linear iterations at : 22:57:55 total time elapsed so far: 5.080000 # loops : 50 mean,max change (kT/e) : 2.2745897E-05 6.2532425E-03 energy calculations done at 5.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.300000 DelPhi exited at 22:57:56 5.305u 0.459s 0:06.06 94.8% 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 Sun Oct 9 2011 at 22:57:56 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.507559 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): -21.94100 31.48900 ymin,ymax (A): -88.03900 -17.19600 zmin,zma (A): -64.11700 -0.2750000 x,y,z range (A): 53.43000 70.84300 63.84200 scale (grids/A): 1.507559 object centre (A): 4.774000 -52.61750 -32.19600 number of atom coordinates read : 4305 total number of charged atoms : 4145 net assigned charge : 2.000011 assigned positive charge : 650.3268 centred at (gu) : 88.53084 87.43281 95.36414 assigned negative charge : -648.3315 centred at (gu) : 88.85861 87.47986 95.52658 start vw surface at 0.2000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 79950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41189 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 23199 mr = 53134 m= 1885 mr = 15087 m= 28 mr = 778 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8400000 number of dielectric boundary points 36063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 572 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 30996 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) : 0.5025197 object centre at (A) : 4.774000 -52.61750 -32.19600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8268835E-03 5.9888414E-03 midg,1,midg; midg,igrid,midg 9.9673001E-03 1.7419677E-02 1,midg,midg; igrid,midg,midg -8.0847321E-04 -8.4693022E-03 gauss-seidel spectral radius is 0.9980154 estimated iterations to convergence 178 setup time was (sec) 1.190000 now iterating at: 22:57:57 rms-change max change #iterations 3.413068 149.7542 at 10iterations 1.364766 53.43256 at 20iterations 0.5441038 22.34064 at 30iterations 0.2175903 8.087125 at 40iterations 8.7099500E-02 3.318271 at 50iterations 3.4908123E-02 1.207812 at 60iterations 1.4029530E-02 0.4586048 at 70iterations 5.6447187E-03 0.1971501 at 80iterations 2.2870603E-03 8.0190182E-02 at 90iterations 9.4998046E-04 3.5477638E-02 at 100iterations 4.1669552E-04 1.6868591E-02 at 110iterations 2.0487937E-04 1.0013580E-02 at 120iterations finished qdiffx linear iterations at : 22:58:08 total time elapsed so far: 12.13000 # loops : 120 mean,max change (kT/e) : 2.0487937E-04 1.0013580E-02 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 22:58:09 12.363u 0.522s 0:13.34 96.5% 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 22:58:09 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.261338 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): -21.94100 31.48900 ymin,ymax (A): -88.03900 -17.19600 zmin,zma (A): -64.11700 -0.2750000 x,y,z range (A): 53.43000 70.84300 63.84200 scale (grids/A): 2.261338 object centre (A): 4.774000 -52.61750 -32.19600 number of atom coordinates read : 4305 total number of charged atoms : 4145 net assigned charge : 2.000011 assigned positive charge : 650.3268 centred at (gu) : 87.79583 86.14871 98.04592 assigned negative charge : -648.3315 centred at (gu) : 88.28772 86.21976 98.28980 start vw surface at 0.2100000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 185994 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41189 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 83033 mr = 130962 m= 20714 mr = 63869 m= 2702 mr = 14730 m= 134 mr = 1597 m= 1 mr = 53 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.050000 number of dielectric boundary points 81368 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 33050 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) : 1.507559 object centre at (A) : 4.774000 -52.61750 -32.19600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1125237 0.1902087 midg,1,midg; midg,igrid,midg 0.3412348 0.4675320 1,midg,midg; igrid,midg,midg -2.0999219E-02 -0.1340747 gauss-seidel spectral radius is 0.9991261 estimated iterations to convergence 267 setup time was (sec) 2.450000 now iterating at: 22:58:12 rms-change max change #iterations 9.538735 307.1481 at 10iterations 5.463871 139.0727 at 20iterations 3.084555 75.29255 at 30iterations 1.730588 37.40198 at 40iterations 0.9638718 23.73494 at 50iterations 0.5380058 11.48653 at 60iterations 0.2974004 6.244331 at 70iterations 0.1643485 3.655167 at 80iterations 9.0941317E-02 1.948159 at 90iterations 5.0019857E-02 1.059326 at 100iterations 2.7521569E-02 0.5517902 at 110iterations 1.5131002E-02 0.2997284 at 120iterations 8.3145872E-03 0.1654387 at 130iterations 4.5983628E-03 0.1027775 at 140iterations 2.5396019E-03 4.8029184E-02 at 150iterations 1.4140001E-03 2.7702332E-02 at 160iterations 8.0116873E-04 1.7881393E-02 at 170iterations 4.6615524E-04 1.0004997E-02 at 180iterations finished qdiffx linear iterations at : 22:58:30 total time elapsed so far: 20.03000 # loops : 180 mean,max change (kT/e) : 4.6615524E-04 1.0004997E-02 energy calculations done at 20.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.25000 DelPhi exited at 22:58:30 20.256u 0.535s 0:21.20 98.0% 0+0k 0+0io 0pf+0w