Tue Oct 11 04:51:35 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 04:51:35 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: HIR 57 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6294757 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): -72.58600 -16.41100 ymin,ymax (A): -48.76700 0.6270000 zmin,zma (A): 4.446000 61.00100 x,y,z range (A): 56.17500 49.39400 56.55500 scale (grids/A): 0.6294757 object centre (A): -44.49850 -24.07000 32.72350 number of atom coordinates read : 2859 total number of charged atoms : 2712 net assigned charge : 8.014020 assigned positive charge : 439.8216 centred at (gu) : 90.63563 90.40325 90.90957 assigned negative charge : -431.8083 centred at (gu) : 90.60094 90.13329 90.81204 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7515 nv = 96 ne = 84 npr = 56501 no. pairs analyzed = 56501 no. exposed pairs = 3751 no. arc points = 25316 no. surface atoms = 1259 nbur = 1600 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 4039 m= 2 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3400000 number of dielectric boundary points 3850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2503 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9078 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.8755309E-10 2.1597321E-08 midg,1,midg; midg,igrid,midg -1.6960936E-08 3.6892889E-08 1,midg,midg; igrid,midg,midg 4.4035491E-09 1.3433533E-08 gauss-seidel spectral radius is 0.9869509 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 04:51:36 rms-change max change #iterations 0.1471275 23.23678 at 10iterations 1.3825070E-02 2.159790 at 20iterations 1.3616642E-03 0.2158051 at 30iterations 1.3440405E-04 1.8435478E-02 at 40iterations 1.5190360E-05 2.8495789E-03 at 50iterations finished qdiffx linear iterations at : 04:51:38 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.5190360E-05 2.8495789E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 04:51:39 3.416u 0.152s 0:04.11 86.6% 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 Tue Oct 11 2011 at 04:51:39 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: HIR 57 has a net charge of 0.5140 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: 1.888427 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): -72.58600 -16.41100 ymin,ymax (A): -48.76700 0.6270000 zmin,zma (A): 4.446000 61.00100 x,y,z range (A): 56.17500 49.39400 56.55500 scale (grids/A): 1.888427 object centre (A): -44.49850 -24.07000 32.72350 number of atom coordinates read : 2859 total number of charged atoms : 2712 net assigned charge : 8.014020 assigned positive charge : 439.8216 centred at (gu) : 91.90629 91.20921 92.72824 assigned negative charge : -431.8083 centred at (gu) : 91.80263 90.39975 92.43578 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 80291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25316 grid for indexing accessible points = 1.400000 m= 29475 mr = 54849 m= 4801 mr = 21379 m= 258 mr = 2948 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1216 time to turn everything in is 0.6400000 number of dielectric boundary points 35577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 175 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21250 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) : 0.6294757 object centre at (A) : -44.49850 -24.07000 32.72350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9272178E-02 4.4770434E-02 midg,1,midg; midg,igrid,midg -2.9942296E-02 5.9793338E-02 1,midg,midg; igrid,midg,midg -4.3551773E-03 -1.1907917E-02 gauss-seidel spectral radius is 0.9986464 estimated iterations to convergence 215 setup time was (sec) 0.9200000 now iterating at: 04:51:40 rms-change max change #iterations 4.484502 184.8073 at 10iterations 2.102863 86.55709 at 20iterations 0.9880720 35.38838 at 30iterations 0.4654734 13.39205 at 40iterations 0.2181139 6.622826 at 50iterations 0.1021234 3.434231 at 60iterations 4.8277274E-02 1.552746 at 70iterations 2.2697618E-02 0.6795936 at 80iterations 1.0644447E-02 0.3388443 at 90iterations 5.0026048E-03 0.1767578 at 100iterations 2.3665091E-03 7.6385498E-02 at 110iterations 1.1123553E-03 3.4480572E-02 at 120iterations finished qdiffx linear iterations at : 04:51:47 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 1.1123553E-03 3.4480572E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 04:51:47 7.540u 0.163s 0:08.23 93.5% 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 Tue Oct 11 2011 at 04:51:48 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: HIR 57 has a net charge of 0.5140 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: 2.832641 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): -72.58600 -16.41100 ymin,ymax (A): -48.76700 0.6270000 zmin,zma (A): 4.446000 61.00100 x,y,z range (A): 56.17500 49.39400 56.55500 scale (grids/A): 2.832641 object centre (A): -44.49850 -24.07000 32.72350 number of atom coordinates read : 2859 total number of charged atoms : 2712 net assigned charge : 8.014020 assigned positive charge : 439.8216 centred at (gu) : 92.85931 91.81364 94.09218 assigned negative charge : -431.8083 centred at (gu) : 92.70377 90.59943 93.65369 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 185481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25316 grid for indexing accessible points = 1.400000 m= 94326 mr = 133158 m= 34744 mr = 76036 m= 8468 mr = 27656 m= 1128 mr = 6315 m= 61 mr = 704 m= 0 mr = 19 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 4286 time to turn everything in is 1.530000 number of dielectric boundary points 80320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 21691 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) : 1.888427 object centre at (A) : -44.49850 -24.07000 32.72350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1283065 0.3569313 midg,1,midg; midg,igrid,midg -0.3387794 0.5168561 1,midg,midg; igrid,midg,midg -0.1982998 -0.1360946 gauss-seidel spectral radius is 0.9992679 estimated iterations to convergence 292 setup time was (sec) 1.830000 now iterating at: 04:51:50 rms-change max change #iterations 10.48882 350.7962 at 10iterations 6.155737 125.1997 at 20iterations 3.587125 83.25771 at 30iterations 2.089957 42.08545 at 40iterations 1.210714 23.56342 at 50iterations 0.7039510 13.47663 at 60iterations 0.4080168 7.398880 at 70iterations 0.2357741 4.079960 at 80iterations 0.1362924 2.506111 at 90iterations 7.8803860E-02 1.489225 at 100iterations 4.5541521E-02 0.7951412 at 110iterations 2.6329948E-02 0.4517403 at 120iterations 1.5185678E-02 0.2706442 at 130iterations 8.7543372E-03 0.1589804 at 140iterations 5.0753918E-03 9.1667175E-02 at 150iterations 2.9348934E-03 5.9089661E-02 at 160iterations 1.6961477E-03 3.0658722E-02 at 170iterations 9.8044553E-04 1.8672943E-02 at 180iterations finished qdiffx linear iterations at : 04:52:00 total time elapsed so far: 12.13000 # loops : 180 mean,max change (kT/e) : 9.8044553E-04 1.8672943E-02 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 04:52:01 12.315u 0.179s 0:13.03 95.7% 0+0k 0+0io 0pf+0w