Sun Oct 9 13:22:18 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 13:22:18 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 0.6729933 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): -7.228000 44.36000 ymin,ymax (A): -14.29100 38.60700 zmin,zma (A): 1.434000 44.76600 x,y,z range (A): 51.58800 52.89800 43.33200 scale (grids/A): 0.6729933 object centre (A): 18.56600 12.15800 23.10000 number of atom coordinates read : 2402 total number of charged atoms : 2256 net assigned charge : 3.406025 assigned positive charge : 367.6961 centred at (gu) : 89.86028 90.75874 90.81311 assigned negative charge : -364.2905 centred at (gu) : 89.84142 90.93160 90.88939 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7324 nv = 96 ne = 84 npr = 48338 no. pairs analyzed = 48338 no. exposed pairs = 3016 no. arc points = 20951 no. surface atoms = 1016 nbur = 1386 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4048 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2065 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8505 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7367197E-08 -8.3712353E-09 midg,1,midg; midg,igrid,midg 4.8340254E-08 -3.8156767E-08 1,midg,midg; igrid,midg,midg 8.1864346E-09 1.7180877E-08 gauss-seidel spectral radius is 0.9885346 estimated iterations to convergence 76 setup time was (sec) 0.5400000 now iterating at: 13:22:19 rms-change max change #iterations 0.1726976 25.54768 at 10iterations 2.0047899E-02 2.979017 at 20iterations 2.9459130E-03 0.4264030 at 30iterations 7.9392979E-04 0.1185493 at 40iterations 2.8638798E-04 4.2125702E-02 at 50iterations finished qdiffx linear iterations at : 13:22:21 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 2.8638798E-04 4.2125702E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 13:22:22 3.418u 0.143s 0:03.84 92.4% 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 13:22:22 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 2.018980 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): -7.228000 44.36000 ymin,ymax (A): -14.29100 38.60700 zmin,zma (A): 1.434000 44.76600 x,y,z range (A): 51.58800 52.89800 43.33200 scale (grids/A): 2.018980 object centre (A): 18.56600 12.15800 23.10000 number of atom coordinates read : 2402 total number of charged atoms : 2256 net assigned charge : 3.406025 assigned positive charge : 367.6961 centred at (gu) : 89.58029 92.27575 92.43900 assigned negative charge : -364.2905 centred at (gu) : 89.52387 92.79436 92.66795 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 77521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20951 grid for indexing accessible points = 1.400000 m= 29528 mr = 53702 m= 5182 mr = 21816 m= 403 mr = 3280 m= 7 mr = 201 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 118 time to turn everything in is 0.6100000 number of dielectric boundary points 33642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 17858 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) : 0.6729933 object centre at (A) : 18.56600 12.15800 23.10000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0061992E-02 9.0747410E-03 midg,1,midg; midg,igrid,midg 1.3264991E-02 -5.4505628E-02 1,midg,midg; igrid,midg,midg 3.6687285E-02 9.5966551E-03 gauss-seidel spectral radius is 0.9987610 estimated iterations to convergence 225 setup time was (sec) 0.9000000 now iterating at: 13:22:23 rms-change max change #iterations 4.598615 183.7693 at 10iterations 2.227795 69.02775 at 20iterations 1.085757 35.94675 at 30iterations 0.5280048 16.29609 at 40iterations 0.2560444 7.652105 at 50iterations 0.1244253 3.707695 at 60iterations 6.0982253E-02 1.960123 at 70iterations 2.9760972E-02 0.8487320 at 80iterations 1.4778560E-02 0.4656982 at 90iterations 7.4884910E-03 0.2338200 at 100iterations 3.9452435E-03 0.1267776 at 110iterations 2.2066024E-03 6.9679260E-02 at 120iterations finished qdiffx linear iterations at : 13:22:29 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 2.2066024E-03 6.9679260E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 13:22:30 7.698u 0.165s 0:08.25 95.1% 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 13:22:30 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 3.028470 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): -7.228000 44.36000 ymin,ymax (A): -14.29100 38.60700 zmin,zma (A): 1.434000 44.76600 x,y,z range (A): 51.58800 52.89800 43.33200 scale (grids/A): 3.028470 object centre (A): 18.56600 12.15800 23.10000 number of atom coordinates read : 2402 total number of charged atoms : 2256 net assigned charge : 3.406025 assigned positive charge : 367.6961 centred at (gu) : 89.37047 93.41361 93.65835 assigned negative charge : -364.2905 centred at (gu) : 89.28573 94.19156 94.00183 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 178763 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20951 grid for indexing accessible points = 1.400000 m= 93334 mr = 129873 m= 35944 mr = 76366 m= 9655 mr = 28980 m= 1758 mr = 7277 m= 161 mr = 1232 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 414 time to turn everything in is 1.520000 number of dielectric boundary points 75789 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 18044 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) : 2.018980 object centre at (A) : 18.56600 12.15800 23.10000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4165145 -6.0176953E-05 midg,1,midg; midg,igrid,midg 0.3061367 -0.6025392 1,midg,midg; igrid,midg,midg 0.4273823 -0.1463199 gauss-seidel spectral radius is 0.9992824 estimated iterations to convergence 295 setup time was (sec) 1.840000 now iterating at: 13:22:32 rms-change max change #iterations 10.54733 403.9238 at 10iterations 6.223958 120.5598 at 20iterations 3.670951 75.86488 at 30iterations 2.155771 42.32699 at 40iterations 1.266424 24.97474 at 50iterations 0.7391012 12.95321 at 60iterations 0.4330508 7.656929 at 70iterations 0.2528704 4.876074 at 80iterations 0.1470638 2.845522 at 90iterations 8.5990854E-02 1.527058 at 100iterations 5.0373688E-02 0.8838266 at 110iterations 2.9618138E-02 0.5227839 at 120iterations 1.7625514E-02 0.3312683 at 130iterations 1.0747087E-02 0.2209530 at 140iterations 6.7905840E-03 0.1354980 at 150iterations 4.5370082E-03 9.3227386E-02 at 160iterations 3.2488308E-03 6.8141937E-02 at 170iterations 2.4654684E-03 5.1479340E-02 at 180iterations finished qdiffx linear iterations at : 13:22:43 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 2.4654684E-03 5.1479340E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.56000 DelPhi exited at 13:22:43 12.559u 0.190s 0:13.27 96.0% 0+0k 0+0io 0pf+0w