Sun Oct 9 07:49:32 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 07:49:32 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 0.6972327 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): -16.39100 31.14000 ymin,ymax (A): -20.27900 30.78000 zmin,zma (A): -4.483000 34.78100 x,y,z range (A): 47.53100 51.05900 39.26400 scale (grids/A): 0.6972327 object centre (A): 7.374499 5.250500 15.14900 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000018 assigned positive charge : 333.8635 centred at (gu) : 89.85925 90.47601 90.80328 assigned negative charge : -327.8639 centred at (gu) : 89.77255 90.56010 90.92688 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7231 nv = 96 ne = 84 npr = 45795 no. pairs analyzed = 45795 no. exposed pairs = 2787 no. arc points = 19966 no. surface atoms = 944 nbur = 1267 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 483 mr = 3966 m= 2 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.1700000 number of dielectric boundary points 3683 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1884 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8206 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7468137E-08 -1.3644510E-08 midg,1,midg; midg,igrid,midg 6.8100370E-08 5.7296923E-09 1,midg,midg; igrid,midg,midg 4.3902206E-09 7.3735229E-08 gauss-seidel spectral radius is 0.9892985 estimated iterations to convergence 79 setup time was (sec) 0.3700000 now iterating at: 07:49:33 rms-change max change #iterations 0.1962422 29.06345 at 10iterations 2.3039293E-02 3.709140 at 20iterations 2.7488305E-03 0.3648146 at 30iterations 3.3443814E-04 4.6516418E-02 at 40iterations 3.9259317E-05 5.9165955E-03 at 50iterations finished qdiffx linear iterations at : 07:49:36 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 3.9259317E-05 5.9165955E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 07:49:36 3.366u 0.173s 0:03.85 91.6% 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 Sun Oct 9 2011 at 07:49:36 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 2.091698 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): -16.39100 31.14000 ymin,ymax (A): -20.27900 30.78000 zmin,zma (A): -4.483000 34.78100 x,y,z range (A): 47.53100 51.05900 39.26400 scale (grids/A): 2.091698 object centre (A): 7.374499 5.250500 15.14900 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000018 assigned positive charge : 333.8635 centred at (gu) : 89.57771 91.42750 92.40957 assigned negative charge : -327.8639 centred at (gu) : 89.31767 91.68021 92.78065 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76251 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19966 grid for indexing accessible points = 1.400000 m= 30219 mr = 52232 m= 5930 mr = 22841 m= 595 mr = 3933 m= 23 mr = 286 m= 0 mr = 7 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2820 time to turn everything in is 0.3800000 number of dielectric boundary points 33719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 16454 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) : 0.6972327 object centre at (A) : 7.374499 5.250500 15.14900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9102088E-02 1.0152474E-02 midg,1,midg; midg,igrid,midg 3.4484942E-02 2.3152536E-02 1,midg,midg; igrid,midg,midg -6.0537187E-03 3.2889131E-02 gauss-seidel spectral radius is 0.9988199 estimated iterations to convergence 230 setup time was (sec) 0.5900000 now iterating at: 07:49:37 rms-change max change #iterations 4.723288 223.5495 at 10iterations 2.311557 91.24355 at 20iterations 1.142134 40.78579 at 30iterations 0.5660439 18.77341 at 40iterations 0.2792944 8.461868 at 50iterations 0.1374503 4.216431 at 60iterations 6.8103716E-02 2.093513 at 70iterations 3.3610903E-02 0.9524994 at 80iterations 1.6530611E-02 0.5871410 at 90iterations 8.1748012E-03 0.2588043 at 100iterations 4.0477966E-03 0.1368232 at 110iterations 1.9943928E-03 5.6758881E-02 at 120iterations finished qdiffx linear iterations at : 07:49:44 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 1.9943928E-03 5.6758881E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 07:49:44 7.817u 0.221s 0:08.32 96.5% 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 Sun Oct 9 2011 at 07:49:44 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 3.137547 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): -16.39100 31.14000 ymin,ymax (A): -20.27900 30.78000 zmin,zma (A): -4.483000 34.78100 x,y,z range (A): 47.53100 51.05900 39.26400 scale (grids/A): 3.137547 object centre (A): 7.374499 5.250500 15.14900 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000018 assigned positive charge : 333.8635 centred at (gu) : 89.36646 92.14131 93.61425 assigned negative charge : -327.8639 centred at (gu) : 88.97647 92.52026 94.17097 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 175356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19966 grid for indexing accessible points = 1.400000 m= 93114 mr = 125605 m= 38494 mr = 76937 m= 11462 mr = 31799 m= 2333 mr = 8846 m= 323 mr = 1602 m= 23 mr = 230 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 9018 time to turn everything in is 1.170000 number of dielectric boundary points 76071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 16592 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) : 2.091698 object centre at (A) : 7.374499 5.250500 15.14900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5691764 5.0537579E-02 midg,1,midg; midg,igrid,midg 0.3345956 0.3159995 1,midg,midg; igrid,midg,midg 1.1680033E-05 0.2478594 gauss-seidel spectral radius is 0.9992909 estimated iterations to convergence 296 setup time was (sec) 1.420000 now iterating at: 07:49:46 rms-change max change #iterations 10.43370 387.4034 at 10iterations 6.064013 122.8923 at 20iterations 3.526354 69.24269 at 30iterations 2.046356 37.70330 at 40iterations 1.190250 19.74451 at 50iterations 0.6922235 11.81416 at 60iterations 0.4020347 7.243306 at 70iterations 0.2336435 3.924747 at 80iterations 0.1354357 2.511357 at 90iterations 7.8604832E-02 1.420002 at 100iterations 4.5712419E-02 0.8462715 at 110iterations 2.6508261E-02 0.4991989 at 120iterations 1.5375481E-02 0.2621708 at 130iterations 8.9462036E-03 0.1539660 at 140iterations 5.1760194E-03 8.8976622E-02 at 150iterations 3.0116478E-03 5.4616928E-02 at 160iterations 1.7496720E-03 3.1558037E-02 at 170iterations 1.0132586E-03 1.7883301E-02 at 180iterations finished qdiffx linear iterations at : 07:49:58 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 1.0132586E-03 1.7883301E-02 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 07:49:58 13.149u 0.198s 0:13.62 97.8% 0+0k 0+0io 0pf+0w