Sun Oct 9 12:38:25 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 12:38:25 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 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: 0.6748687 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): -5.601000 44.28400 ymin,ymax (A): -14.14600 38.60500 zmin,zma (A): 2.912000 45.54600 x,y,z range (A): 49.88499 52.75100 42.63400 scale (grids/A): 0.6748687 object centre (A): 19.34150 12.22950 24.22900 number of atom coordinates read : 2383 total number of charged atoms : 2242 net assigned charge : 4.500021 assigned positive charge : 365.7711 centred at (gu) : 89.45055 90.45599 90.26359 assigned negative charge : -361.2716 centred at (gu) : 89.42814 90.60895 90.32809 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7312 nv = 96 ne = 84 npr = 47671 no. pairs analyzed = 47671 no. exposed pairs = 3074 no. arc points = 21306 no. surface atoms = 1019 nbur = 1364 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 440 mr = 3979 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2063 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8395 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2629892E-08 -1.2284450E-10 midg,1,midg; midg,igrid,midg 5.2415199E-08 -2.6773622E-08 1,midg,midg; igrid,midg,midg 1.2538649E-08 2.0857321E-08 gauss-seidel spectral radius is 0.9885976 estimated iterations to convergence 76 setup time was (sec) 0.4900000 now iterating at: 12:38:26 rms-change max change #iterations 0.1753161 30.55106 at 10iterations 1.9845590E-02 2.523564 at 20iterations 2.7653836E-03 0.4816475 at 30iterations 6.2863244E-04 0.1106567 at 40iterations 1.9592827E-04 3.3752441E-02 at 50iterations finished qdiffx linear iterations at : 12:38:28 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 1.9592827E-04 3.3752441E-02 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 12:38:29 3.054u 0.164s 0:03.55 90.4% 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 Sun Oct 9 2011 at 12:38:29 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.024606 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): -5.601000 44.28400 ymin,ymax (A): -14.14600 38.60500 zmin,zma (A): 2.912000 45.54600 x,y,z range (A): 49.88499 52.75100 42.63400 scale (grids/A): 2.024606 object centre (A): 19.34150 12.22950 24.22900 number of atom coordinates read : 2383 total number of charged atoms : 2242 net assigned charge : 4.500021 assigned positive charge : 365.7711 centred at (gu) : 88.35118 91.36762 90.79029 assigned negative charge : -361.2716 centred at (gu) : 88.28422 91.82664 90.98405 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78071 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21306 grid for indexing accessible points = 1.400000 m= 29963 mr = 53966 m= 4998 mr = 22058 m= 400 mr = 3092 m= 2 mr = 173 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 34145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17715 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) : 0.6748687 object centre at (A) : 19.34150 12.22950 24.22900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3780532E-02 9.5192026E-03 midg,1,midg; midg,igrid,midg 1.7727165E-02 -2.9849589E-02 1,midg,midg; igrid,midg,midg 3.2778155E-02 4.8093400E-03 gauss-seidel spectral radius is 0.9987700 estimated iterations to convergence 226 setup time was (sec) 0.8200000 now iterating at: 12:38:30 rms-change max change #iterations 4.643064 219.7373 at 10iterations 2.242004 79.58244 at 20iterations 1.094562 33.16051 at 30iterations 0.5315243 15.76594 at 40iterations 0.2581033 7.971926 at 50iterations 0.1259488 3.810416 at 60iterations 6.1642144E-02 1.779804 at 70iterations 3.0052735E-02 0.8983612 at 80iterations 1.4858824E-02 0.4101963 at 90iterations 7.3496550E-03 0.2166061 at 100iterations 3.7269527E-03 0.1151047 at 110iterations 1.9694348E-03 6.4025879E-02 at 120iterations finished qdiffx linear iterations at : 12:38:35 total time elapsed so far: 6.670000 # loops : 120 mean,max change (kT/e) : 1.9694348E-03 6.4025879E-02 energy calculations done at 6.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.840000 DelPhi exited at 12:38:36 6.846u 0.148s 0:07.29 95.7% 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 12:38:36 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 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: 3.036909 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): -5.601000 44.28400 ymin,ymax (A): -14.14600 38.60500 zmin,zma (A): 2.912000 45.54600 x,y,z range (A): 49.88499 52.75100 42.63400 scale (grids/A): 3.036909 object centre (A): 19.34150 12.22950 24.22900 number of atom coordinates read : 2383 total number of charged atoms : 2242 net assigned charge : 4.500021 assigned positive charge : 365.7711 centred at (gu) : 87.52662 92.05128 91.18530 assigned negative charge : -361.2716 centred at (gu) : 87.42633 92.73997 91.47601 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 179908 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21306 grid for indexing accessible points = 1.400000 m= 94512 mr = 130196 m= 36000 mr = 77282 m= 9034 mr = 28861 m= 1586 mr = 6689 m= 123 mr = 1102 m= 3 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.400000 number of dielectric boundary points 76974 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 17934 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) : 2.024606 object centre at (A) : 19.34150 12.22950 24.22900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4094897 9.9287182E-03 midg,1,midg; midg,igrid,midg 0.4487092 -0.3858610 1,midg,midg; igrid,midg,midg 0.3580595 -0.1312203 gauss-seidel spectral radius is 0.9992844 estimated iterations to convergence 295 setup time was (sec) 1.670000 now iterating at: 12:38:38 rms-change max change #iterations 10.55943 407.2403 at 10iterations 6.212923 149.1741 at 20iterations 3.662727 88.39703 at 30iterations 2.153994 42.51995 at 40iterations 1.262536 26.28983 at 50iterations 0.7376097 14.85511 at 60iterations 0.4315676 7.784245 at 70iterations 0.2517445 4.450890 at 80iterations 0.1468173 2.901217 at 90iterations 8.5653260E-02 1.543106 at 100iterations 5.0089601E-02 0.8830851 at 110iterations 2.9364120E-02 0.6126022 at 120iterations 1.7372645E-02 0.3384380 at 130iterations 1.0407188E-02 0.1872635 at 140iterations 6.4221588E-03 0.1317825 at 150iterations 4.1335169E-03 9.2372894E-02 at 160iterations 2.8277910E-03 6.4270020E-02 at 170iterations 2.0565938E-03 4.5837402E-02 at 180iterations finished qdiffx linear iterations at : 12:38:47 total time elapsed so far: 10.95000 # loops : 180 mean,max change (kT/e) : 2.0565938E-03 4.5837402E-02 energy calculations done at 10.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.13000 DelPhi exited at 12:38:48 11.128u 0.161s 0:11.55 97.6% 0+0k 0+0io 0pf+0w