Tue Oct 11 06:33:33 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 Tue Oct 11 2011 at 06:33:33 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7071068 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): -18.74100 25.25800 ymin,ymax (A): -28.58100 11.08400 zmin,zma (A): -13.69600 36.65000 x,y,z range (A): 43.99900 39.66500 50.34600 scale (grids/A): 0.7071068 object centre (A): 3.258501 -8.748501 11.47700 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.931010 assigned positive charge : 317.5340 centred at (gu) : 89.37231 90.63544 89.29057 assigned negative charge : -311.6031 centred at (gu) : 89.22414 90.60689 89.22868 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7018 nv = 96 ne = 84 npr = 42287 no. pairs analyzed = 42287 no. exposed pairs = 2509 no. arc points = 16977 no. surface atoms = 856 nbur = 1233 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 434 mr = 4059 m= 8 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2900000 number of dielectric boundary points 3326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1660 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7893 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2378028E-08 7.0216487E-08 midg,1,midg; midg,igrid,midg 3.2318638E-08 7.2578139E-08 1,midg,midg; igrid,midg,midg -2.6875160E-08 1.0783600E-07 gauss-seidel spectral radius is 0.9895727 estimated iterations to convergence 80 setup time was (sec) 0.5700000 now iterating at: 06:33:34 rms-change max change #iterations 0.1999729 26.39062 at 10iterations 2.5348678E-02 3.458160 at 20iterations 3.2741602E-03 0.4283066 at 30iterations 5.0066772E-04 6.8916321E-02 at 40iterations 1.0610130E-04 1.5403748E-02 at 50iterations finished qdiffx linear iterations at : 06:33:37 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 1.0610130E-04 1.5403748E-02 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 06:33:38 4.032u 0.267s 0:04.80 89.3% 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 06:33:38 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.121320 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): -18.74100 25.25800 ymin,ymax (A): -28.58100 11.08400 zmin,zma (A): -13.69600 36.65000 x,y,z range (A): 43.99900 39.66500 50.34600 scale (grids/A): 2.121320 object centre (A): 3.258501 -8.748501 11.47700 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.931010 assigned positive charge : 317.5340 centred at (gu) : 88.11697 91.90642 87.87168 assigned negative charge : -311.6031 centred at (gu) : 87.67249 91.82079 87.68603 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 74976 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16977 grid for indexing accessible points = 1.400000 m= 29579 mr = 53747 m= 5614 mr = 22435 m= 534 mr = 3777 m= 21 mr = 294 m= 0 mr = 5 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 285 time to turn everything in is 0.7000000 number of dielectric boundary points 30466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15533 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) : 0.7071068 object centre at (A) : 3.258501 -8.748501 11.47700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2564194E-02 3.9526224E-02 midg,1,midg; midg,igrid,midg 4.3255575E-03 3.3518098E-02 1,midg,midg; igrid,midg,midg 1.4927230E-02 3.1244298E-02 gauss-seidel spectral radius is 0.9988275 estimated iterations to convergence 231 setup time was (sec) 1.000000 now iterating at: 06:33:39 rms-change max change #iterations 4.621281 218.4838 at 10iterations 2.282679 82.27797 at 20iterations 1.133221 34.53329 at 30iterations 0.5597520 17.09071 at 40iterations 0.2779908 8.661297 at 50iterations 0.1379593 3.951805 at 60iterations 6.8467565E-02 2.061722 at 70iterations 3.4016360E-02 1.022616 at 80iterations 1.6994413E-02 0.5010829 at 90iterations 8.4798075E-03 0.2494202 at 100iterations 4.2531909E-03 0.1246567 at 110iterations 2.1498585E-03 6.6535950E-02 at 120iterations finished qdiffx linear iterations at : 06:33:47 total time elapsed so far: 9.260000 # loops : 120 mean,max change (kT/e) : 2.1498585E-03 6.6535950E-02 energy calculations done at 9.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.440000 DelPhi exited at 06:33:48 9.447u 0.256s 0:10.10 95.9% 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 06:33:48 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.181981 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): -18.74100 25.25800 ymin,ymax (A): -28.58100 11.08400 zmin,zma (A): -13.69600 36.65000 x,y,z range (A): 43.99900 39.66500 50.34600 scale (grids/A): 3.181981 object centre (A): 3.258501 -8.748501 11.47700 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.931010 assigned positive charge : 317.5340 centred at (gu) : 87.17551 92.85961 86.80756 assigned negative charge : -311.6031 centred at (gu) : 86.50865 92.73119 86.52908 start vw surface at 0.1600000 fill in re-entrant regions at 1.000000 boundary points on vw surface= 172880 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16977 grid for indexing accessible points = 1.400000 m= 92854 mr = 129195 m= 37073 mr = 77387 m= 10707 mr = 30525 m= 2173 mr = 8330 m= 290 mr = 1592 m= 19 mr = 213 m= 0 mr = 13 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 917 time to turn everything in is 2.210000 number of dielectric boundary points 68741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.360000 number of grid points assigned charge 15639 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) : 2.121320 object centre at (A) : 3.258501 -8.748501 11.47700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7331565 0.3409158 midg,1,midg; midg,igrid,midg 2.0406246E-02 0.2842363 1,midg,midg; igrid,midg,midg 0.3894501 0.2814845 gauss-seidel spectral radius is 0.9992928 estimated iterations to convergence 297 setup time was (sec) 2.530000 now iterating at: 06:33:51 rms-change max change #iterations 10.25502 402.1770 at 10iterations 6.051188 123.3192 at 20iterations 3.555010 70.89756 at 30iterations 2.091514 36.85649 at 40iterations 1.227119 21.91382 at 50iterations 0.7203931 15.18030 at 60iterations 0.4217922 7.435256 at 70iterations 0.2470408 4.644305 at 80iterations 0.1444066 2.726163 at 90iterations 8.4652565E-02 1.520563 at 100iterations 4.9619325E-02 0.8803606 at 110iterations 2.9252820E-02 0.5676041 at 120iterations 1.7317308E-02 0.3349533 at 130iterations 1.0405659E-02 0.2153473 at 140iterations 6.3901315E-03 0.1281147 at 150iterations 4.0449752E-03 7.6950073E-02 at 160iterations 2.6978075E-03 5.3329468E-02 at 170iterations 1.8928626E-03 3.6954880E-02 at 180iterations finished qdiffx linear iterations at : 06:34:04 total time elapsed so far: 16.15000 # loops : 180 mean,max change (kT/e) : 1.8928626E-03 3.6954880E-02 energy calculations done at 16.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.32000 DelPhi exited at 06:34:05 16.326u 0.309s 0:17.11 97.1% 0+0k 0+0io 0pf+0w