Tue Oct 11 08:07:27 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 Tue Oct 11 2011 at 08:07:27 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 = 2344 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: 0.6405643 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): -22.44300 29.51400 ymin,ymax (A): 21.45000 77.02600 zmin,zma (A): 2.645000 52.33900 x,y,z range (A): 51.95700 55.57600 49.69400 scale (grids/A): 0.6405643 object centre (A): 3.535501 49.23800 27.49200 number of atom coordinates read : 2344 total number of charged atoms : 2206 net assigned charge : 4.500012 assigned positive charge : 351.1133 centred at (gu) : 89.97659 87.78379 91.97548 assigned negative charge : -346.6139 centred at (gu) : 89.76373 87.84928 91.92796 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6604 nv = 96 ne = 84 npr = 46942 no. pairs analyzed = 46942 no. exposed pairs = 3023 no. arc points = 21824 no. surface atoms = 1009 nbur = 1335 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 358 mr = 3525 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.1700000 number of dielectric boundary points 3396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2116 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7713 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7757324E-10 1.7238825E-08 midg,1,midg; midg,igrid,midg 2.1198414E-08 -2.4306077E-10 1,midg,midg; igrid,midg,midg -1.6568471E-08 2.8001805E-08 gauss-seidel spectral radius is 0.9873559 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 08:07:28 rms-change max change #iterations 0.1345694 21.76097 at 10iterations 1.3357434E-02 1.832531 at 20iterations 1.3529171E-03 0.1843395 at 30iterations 1.5554622E-04 2.6978493E-02 at 40iterations 3.3281449E-05 7.3328018E-03 at 50iterations finished qdiffx linear iterations at : 08:07:30 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 3.3281449E-05 7.3328018E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 08:07:31 3.319u 0.175s 0:03.90 89.2% 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 Tue Oct 11 2011 at 08:07:31 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 = 2344 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.921693 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): -22.44300 29.51400 ymin,ymax (A): 21.45000 77.02600 zmin,zma (A): 2.645000 52.33900 x,y,z range (A): 51.95700 55.57600 49.69400 scale (grids/A): 1.921693 object centre (A): 3.535501 49.23800 27.49200 number of atom coordinates read : 2344 total number of charged atoms : 2206 net assigned charge : 4.500012 assigned positive charge : 351.1133 centred at (gu) : 89.92921 83.35108 95.92592 assigned negative charge : -346.6139 centred at (gu) : 89.29112 83.54818 95.78380 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 70325 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21824 grid for indexing accessible points = 1.400000 m= 25763 mr = 47497 m= 4241 mr = 18936 m= 284 mr = 2607 m= 6 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 149 time to turn everything in is 0.3300000 number of dielectric boundary points 31458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 17377 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) : 0.6405643 object centre at (A) : 3.535501 49.23800 27.49200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5311317E-03 3.3563349E-02 midg,1,midg; midg,igrid,midg 5.0976038E-02 2.5161913E-02 1,midg,midg; igrid,midg,midg -1.9794786E-02 3.4312159E-02 gauss-seidel spectral radius is 0.9986324 estimated iterations to convergence 214 setup time was (sec) 0.5400000 now iterating at: 08:07:32 rms-change max change #iterations 4.069477 162.5068 at 10iterations 1.893692 66.77261 at 20iterations 0.8837188 32.73660 at 30iterations 0.4147919 13.58883 at 40iterations 0.1930814 6.411409 at 50iterations 9.0119049E-02 3.171112 at 60iterations 4.2090360E-02 1.342468 at 70iterations 1.9728765E-02 0.6287174 at 80iterations 9.2044100E-03 0.2808819 at 90iterations 4.3521500E-03 0.1441879 at 100iterations 2.0405860E-03 6.8095207E-02 at 110iterations 9.7522797E-04 3.4193039E-02 at 120iterations finished qdiffx linear iterations at : 08:07:39 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 9.7522797E-04 3.4193039E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 08:07:39 7.715u 0.213s 0:08.21 96.4% 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 Tue Oct 11 2011 at 08:07:39 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 = 2344 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: 2.882539 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): -22.44300 29.51400 ymin,ymax (A): 21.45000 77.02600 zmin,zma (A): 2.645000 52.33900 x,y,z range (A): 51.95700 55.57600 49.69400 scale (grids/A): 2.882539 object centre (A): 3.535501 49.23800 27.49200 number of atom coordinates read : 2344 total number of charged atoms : 2206 net assigned charge : 4.500012 assigned positive charge : 351.1133 centred at (gu) : 89.89389 80.02646 98.88876 assigned negative charge : -346.6139 centred at (gu) : 88.93657 80.32220 98.67563 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 162520 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21824 grid for indexing accessible points = 1.400000 m= 82057 mr = 115630 m= 30911 mr = 66462 m= 7549 mr = 25017 m= 1249 mr = 5561 m= 113 mr = 856 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 498 time to turn everything in is 0.9300000 number of dielectric boundary points 70824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 17647 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) : 1.921693 object centre at (A) : 3.535501 49.23800 27.49200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9562968E-03 0.3335005 midg,1,midg; midg,igrid,midg 0.4769095 0.5257825 1,midg,midg; igrid,midg,midg -0.1731817 0.4844573 gauss-seidel spectral radius is 0.9992620 estimated iterations to convergence 291 setup time was (sec) 1.160000 now iterating at: 08:07:41 rms-change max change #iterations 9.638855 383.4368 at 10iterations 5.676807 141.1147 at 20iterations 3.327611 77.98792 at 30iterations 1.938533 40.12914 at 40iterations 1.126571 24.08461 at 50iterations 0.6527092 14.95909 at 60iterations 0.3779986 7.845336 at 70iterations 0.2185890 4.492697 at 80iterations 0.1264207 2.268906 at 90iterations 7.2835989E-02 1.359911 at 100iterations 4.1900657E-02 0.8008118 at 110iterations 2.4199005E-02 0.4683857 at 120iterations 1.3931935E-02 0.2666919 at 130iterations 8.0404403E-03 0.1578150 at 140iterations 4.6288730E-03 9.3933105E-02 at 150iterations 2.6699551E-03 4.8376083E-02 at 160iterations 1.5387159E-03 3.0067444E-02 at 170iterations 8.9111755E-04 1.5492916E-02 at 180iterations finished qdiffx linear iterations at : 08:07:52 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 8.9111755E-04 1.5492916E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 08:07:52 12.656u 0.214s 0:13.16 97.7% 0+0k 0+0io 0pf+0w