Sun Oct 9 14:07:37 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 14:07:37 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2415 !!! WARNING: SEP 185 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6628682 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): -6.993000 42.21400 ymin,ymax (A): 21.61200 75.31800 zmin,zma (A): 41.78300 84.72800 x,y,z range (A): 49.20700 53.70600 42.94500 scale (grids/A): 0.6628682 object centre (A): 17.61050 48.46500 63.25550 number of atom coordinates read : 2415 total number of charged atoms : 2271 net assigned charge : 4.025021 assigned positive charge : 372.9611 centred at (gu) : 90.59306 90.81628 90.52162 assigned negative charge : -368.9365 centred at (gu) : 90.60591 90.92561 90.66228 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7031 nv = 96 ne = 84 npr = 48599 no. pairs analyzed = 48599 no. exposed pairs = 3051 no. arc points = 21637 no. surface atoms = 1027 nbur = 1388 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 387 mr = 3757 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2039 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8244 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5426144E-08 -1.9507986E-08 midg,1,midg; midg,igrid,midg 2.8140001E-08 -1.3084158E-08 1,midg,midg; igrid,midg,midg 1.2475671E-08 9.9648600E-09 gauss-seidel spectral radius is 0.9881857 estimated iterations to convergence 75 setup time was (sec) 0.3800000 now iterating at: 14:07:38 rms-change max change #iterations 0.1651460 26.83063 at 10iterations 1.8444970E-02 2.907013 at 20iterations 2.5607061E-03 0.4084835 at 30iterations 5.8701739E-04 9.8983765E-02 at 40iterations 1.8356793E-04 3.1982422E-02 at 50iterations finished qdiffx linear iterations at : 14:07:41 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.8356793E-04 3.1982422E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:07:41 3.390u 0.175s 0:03.89 91.5% 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 14:07:41 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2415 !!! WARNING: SEP 185 has a net charge of -0.4750 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: 1.988605 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): -6.993000 42.21400 ymin,ymax (A): 21.61200 75.31800 zmin,zma (A): 41.78300 84.72800 x,y,z range (A): 49.20700 53.70600 42.94500 scale (grids/A): 1.988605 object centre (A): 17.61050 48.46500 63.25550 number of atom coordinates read : 2415 total number of charged atoms : 2271 net assigned charge : 4.025021 assigned positive charge : 372.9611 centred at (gu) : 91.77894 92.44849 91.56455 assigned negative charge : -368.9365 centred at (gu) : 91.81734 92.77663 91.98646 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75525 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21637 grid for indexing accessible points = 1.400000 m= 27761 mr = 51889 m= 4621 mr = 20192 m= 382 mr = 2775 m= 14 mr = 206 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 33241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17949 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) : 0.6628682 object centre at (A) : 17.61050 48.46500 63.25550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9613997E-02 -8.6143557E-03 midg,1,midg; midg,igrid,midg 5.3282077E-03 -1.1547177E-02 1,midg,midg; igrid,midg,midg 3.1960681E-02 1.0474546E-02 gauss-seidel spectral radius is 0.9987295 estimated iterations to convergence 222 setup time was (sec) 0.6100000 now iterating at: 14:07:42 rms-change max change #iterations 4.529388 183.9217 at 10iterations 2.167029 76.17135 at 20iterations 1.043560 32.55601 at 30iterations 0.4996617 15.14475 at 40iterations 0.2409132 7.230679 at 50iterations 0.1162322 3.588928 at 60iterations 5.5964272E-02 1.716405 at 70iterations 2.7182199E-02 0.8388557 at 80iterations 1.3268228E-02 0.4257774 at 90iterations 6.5625557E-03 0.2208557 at 100iterations 3.3269979E-03 0.1053391 at 110iterations 1.7586215E-03 6.0028076E-02 at 120iterations finished qdiffx linear iterations at : 14:07:49 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 1.7586215E-03 6.0028076E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 14:07:50 7.864u 0.198s 0:08.33 96.6% 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 14:07:50 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2415 !!! WARNING: SEP 185 has a net charge of -0.4750 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: 2.982907 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): -6.993000 42.21400 ymin,ymax (A): 21.61200 75.31800 zmin,zma (A): 41.78300 84.72800 x,y,z range (A): 49.20700 53.70600 42.94500 scale (grids/A): 2.982907 object centre (A): 17.61050 48.46500 63.25550 number of atom coordinates read : 2415 total number of charged atoms : 2271 net assigned charge : 4.025021 assigned positive charge : 372.9611 centred at (gu) : 92.66817 93.67261 92.34659 assigned negative charge : -368.9365 centred at (gu) : 92.72581 94.16486 92.97977 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 174285 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21637 grid for indexing accessible points = 1.400000 m= 88740 mr = 125663 m= 32893 mr = 72000 m= 8401 mr = 26151 m= 1531 mr = 6146 m= 171 mr = 1075 m= 3 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9700000 number of dielectric boundary points 74884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 18166 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) : 1.988605 object centre at (A) : 17.61050 48.46500 63.25550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4809634 -0.1388191 midg,1,midg; midg,igrid,midg 0.1749348 -0.1932533 1,midg,midg; igrid,midg,midg 0.3963079 3.4457261E-03 gauss-seidel spectral radius is 0.9992770 estimated iterations to convergence 293 setup time was (sec) 1.210000 now iterating at: 14:07:51 rms-change max change #iterations 10.49062 424.3648 at 10iterations 6.172574 152.3107 at 20iterations 3.626978 78.04497 at 30iterations 2.120369 43.87434 at 40iterations 1.239474 24.33498 at 50iterations 0.7226976 12.63191 at 60iterations 0.4210667 7.966788 at 70iterations 0.2445692 4.210503 at 80iterations 0.1424548 2.447849 at 90iterations 8.2989372E-02 1.431491 at 100iterations 4.8346065E-02 0.9502349 at 110iterations 2.8346227E-02 0.5137901 at 120iterations 1.6758252E-02 0.2877502 at 130iterations 1.0116355E-02 0.1929550 at 140iterations 6.3089002E-03 0.1382294 at 150iterations 4.1082911E-03 9.1686249E-02 at 160iterations 2.8457285E-03 6.1401367E-02 at 170iterations 2.0909547E-03 4.6722412E-02 at 180iterations finished qdiffx linear iterations at : 14:08:03 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 2.0909547E-03 4.6722412E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 14:08:03 12.752u 0.225s 0:13.24 97.9% 0+0k 0+0io 0pf+0w