Sat Oct 15 13:50:41 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 15 2011 at 13:50:42 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5300301 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): 45.08600 112.2520 ymin,ymax (A): 21.43900 84.48500 zmin,zma (A): 115.9600 174.2830 x,y,z range (A): 67.16600 63.04600 58.32299 scale (grids/A): 0.5300301 object centre (A): 78.66900 52.96200 145.1215 number of atom coordinates read : 2754 total number of charged atoms : 2557 net assigned charge : -12.49998 assigned positive charge : 408.2823 centred at (gu) : 87.66443 90.76652 90.95002 assigned negative charge : -420.7832 centred at (gu) : 87.66954 90.72869 90.69729 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5121 nv = 96 ne = 84 npr = 52508 no. pairs analyzed = 52508 no. exposed pairs = 3994 no. arc points = 29072 no. surface atoms = 1321 nbur = 1433 mkacc time = 0.1900000 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 = 1.596000 m= 194 mr = 2277 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2797 ## 407 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 6615 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0187731E-09 5.3095800E-10 midg,1,midg; midg,igrid,midg -4.4909998E-10 -3.4717257E-10 1,midg,midg; igrid,midg,midg -7.1370820E-10 -2.4440003E-10 gauss-seidel spectral radius is 0.9816584 estimated iterations to convergence 61 setup time was (sec) 0.7200000 now iterating at: 13:50:45 rms-change max change #iterations 5.9392329E-02 13.38162 at 10iterations 3.5897335E-03 0.6896477 at 20iterations 2.3973854E-04 4.5700073E-02 at 30iterations 2.6907150E-05 7.3909760E-03 at 40iterations 5.8367868E-06 1.8091202E-03 at 50iterations finished qdiffx linear iterations at : 13:50:54 total time elapsed so far: 4.780000 # loops : 50 mean,max change (kT/e) : 5.8367868E-06 1.8091202E-03 energy calculations done at 4.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.000000 DelPhi exited at 13:50:55 5.005u 0.502s 0:14.00 39.2% 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 15 2011 at 13:50:56 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.590090 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): 45.08600 112.2520 ymin,ymax (A): 21.43900 84.48500 zmin,zma (A): 115.9600 174.2830 x,y,z range (A): 67.16600 63.04600 58.32299 scale (grids/A): 1.590090 object centre (A): 78.66900 52.96200 145.1215 number of atom coordinates read : 2754 total number of charged atoms : 2557 net assigned charge : -12.49998 assigned positive charge : 408.2823 centred at (gu) : 82.99222 92.29901 92.84946 assigned negative charge : -420.7832 centred at (gu) : 83.00826 92.18559 92.09150 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 56079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29072 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 15965 mr = 34315 m= 1604 mr = 10383 m= 41 mr = 733 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 28258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 345 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19381 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) : 0.5300301 object centre at (A) : 78.66900 52.96200 145.1215 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4772112E-02 1.4282967E-02 midg,1,midg; midg,igrid,midg -1.8663971E-02 -1.2007876E-02 1,midg,midg; igrid,midg,midg -2.5626678E-02 -1.0530422E-02 gauss-seidel spectral radius is 0.9980701 estimated iterations to convergence 181 setup time was (sec) 0.9900000 now iterating at: 13:50:58 rms-change max change #iterations 3.015331 150.9266 at 10iterations 1.210398 54.75113 at 20iterations 0.4865150 19.82925 at 30iterations 0.1969297 8.623312 at 40iterations 7.9601996E-02 3.293523 at 50iterations 3.2181703E-02 1.206432 at 60iterations 1.3024350E-02 0.5046620 at 70iterations 5.2664508E-03 0.1945419 at 80iterations 2.1326444E-03 8.9981079E-02 at 90iterations 8.6379691E-04 3.2889366E-02 at 100iterations 3.5120698E-04 1.4593124E-02 at 110iterations 1.4278686E-04 7.2078705E-03 at 120iterations finished qdiffx linear iterations at : 13:51:15 total time elapsed so far: 11.04000 # loops : 120 mean,max change (kT/e) : 1.4278686E-04 7.2078705E-03 energy calculations done at 11.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.27000 DelPhi exited at 13:51:16 11.272u 0.519s 0:19.96 59.0% 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 15 2011 at 13:51:16 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.385135 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): 45.08600 112.2520 ymin,ymax (A): 21.43900 84.48500 zmin,zma (A): 115.9600 174.2830 x,y,z range (A): 67.16600 63.04600 58.32299 scale (grids/A): 2.385135 object centre (A): 78.66900 52.96200 145.1215 number of atom coordinates read : 2754 total number of charged atoms : 2557 net assigned charge : -12.49998 assigned positive charge : 408.2823 centred at (gu) : 79.48817 93.44842 94.27401 assigned negative charge : -420.7832 centred at (gu) : 79.51228 93.27837 93.13725 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 129800 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29072 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 55450 mr = 84919 m= 15507 mr = 41772 m= 2493 mr = 11340 m= 152 mr = 1558 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.8500001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.480000 number of dielectric boundary points 63788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 20417 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) : 1.590090 object centre at (A) : 78.66900 52.96200 145.1215 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2373144 0.2281421 midg,1,midg; midg,igrid,midg -0.3372058 -0.1038815 1,midg,midg; igrid,midg,midg -0.3865933 -0.1027622 gauss-seidel spectral radius is 0.9990952 estimated iterations to convergence 263 setup time was (sec) 1.940000 now iterating at: 13:51:18 rms-change max change #iterations 8.027198 330.6996 at 10iterations 4.461190 125.3349 at 20iterations 2.453866 74.05132 at 30iterations 1.347313 33.46375 at 40iterations 0.7335079 21.88871 at 50iterations 0.3998530 9.004581 at 60iterations 0.2175081 5.061508 at 70iterations 0.1177128 2.841454 at 80iterations 6.3859604E-02 1.423677 at 90iterations 3.4629140E-02 0.7261925 at 100iterations 1.8749915E-02 0.4370995 at 110iterations 1.0152965E-02 0.2327538 at 120iterations 5.4808185E-03 0.1225128 at 130iterations 2.9611415E-03 6.8773270E-02 at 140iterations 1.6021586E-03 3.5408020E-02 at 150iterations 8.6768193E-04 2.0336151E-02 at 160iterations 4.6868995E-04 1.0410309E-02 at 170iterations 2.5321796E-04 5.8059692E-03 at 180iterations finished qdiffx linear iterations at : 13:51:43 total time elapsed so far: 26.72000 # loops : 180 mean,max change (kT/e) : 2.5321796E-04 5.8059692E-03 energy calculations done at 26.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 26.94000 DelPhi exited at 13:51:44 26.942u 0.513s 0:27.92 98.3% 0+0k 0+0io 0pf+0w