Tue Oct 11 06:02:18 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+sph.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 = amb.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 06:02:18 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2320 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: 0.7241955 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): 25.88100 72.78300 ymin,ymax (A): -18.57800 30.58000 zmin,zma (A): 3.918000 46.56900 x,y,z range (A): 46.90200 49.15800 42.65100 scale (grids/A): 0.7241955 object centre (A): 49.33200 6.001000 25.24350 number of atom coordinates read : 2320 total number of charged atoms : 1996 net assigned charge : 6.500008 assigned positive charge : 324.3239 centred at (gu) : 89.16512 90.46609 90.30276 assigned negative charge : -317.8241 centred at (gu) : 89.30785 90.40897 90.38631 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7583 nv = 96 ne = 84 npr = 42653 no. pairs analyzed = 42653 no. exposed pairs = 2566 no. arc points = 17436 no. surface atoms = 876 nbur = 1444 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 530 mr = 4419 m= 4 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1636 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8239 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3222203E-07 1.9568940E-08 midg,1,midg; midg,igrid,midg 3.5265916E-08 1.3217687E-07 1,midg,midg; igrid,midg,midg 2.1349587E-07 -2.0692557E-08 gauss-seidel spectral radius is 0.9900597 estimated iterations to convergence 82 setup time was (sec) 0.3600000 now iterating at: 06:02:19 rms-change max change #iterations 0.2176771 29.00476 at 10iterations 2.8662818E-02 3.961628 at 20iterations 3.9751013E-03 0.5008755 at 30iterations 6.3931395E-04 8.4705353E-02 at 40iterations 1.5562115E-04 1.8320084E-02 at 50iterations finished qdiffx linear iterations at : 06:02:22 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.5562115E-04 1.8320084E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 06:02:23 3.328u 0.165s 0:04.11 84.6% 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 06:02:23 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2320 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: 2.172586 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): 25.88100 72.78300 ymin,ymax (A): -18.57800 30.58000 zmin,zma (A): 3.918000 46.56900 x,y,z range (A): 46.90200 49.15800 42.65100 scale (grids/A): 2.172586 object centre (A): 49.33200 6.001000 25.24350 number of atom coordinates read : 2320 total number of charged atoms : 1996 net assigned charge : 6.500008 assigned positive charge : 324.3239 centred at (gu) : 87.49540 91.39823 90.90833 assigned negative charge : -317.8241 centred at (gu) : 87.92352 91.22702 91.15897 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79743 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17436 grid for indexing accessible points = 1.400000 m= 33684 mr = 57125 m= 7035 mr = 25980 m= 729 mr = 4844 m= 21 mr = 392 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 32869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15863 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) : 0.7241955 object centre at (A) : 49.33200 6.001000 25.24350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5220715E-02 3.5832666E-02 midg,1,midg; midg,igrid,midg 4.9550422E-02 3.6648303E-02 1,midg,midg; igrid,midg,midg 5.1305085E-02 -6.2914930E-02 gauss-seidel spectral radius is 0.9988796 estimated iterations to convergence 236 setup time was (sec) 0.6300000 now iterating at: 06:02:23 rms-change max change #iterations 4.816435 188.0152 at 10iterations 2.425874 80.71733 at 20iterations 1.224787 40.55013 at 30iterations 0.6152902 19.07342 at 40iterations 0.3104361 9.661816 at 50iterations 0.1559573 4.288972 at 60iterations 7.8918576E-02 2.400486 at 70iterations 3.9647039E-02 1.200272 at 80iterations 2.0146115E-02 0.5954485 at 90iterations 1.0216525E-02 0.3689041 at 100iterations 5.1834323E-03 0.1423864 at 110iterations 2.6770418E-03 8.1573486E-02 at 120iterations finished qdiffx linear iterations at : 06:02:31 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 2.6770418E-03 8.1573486E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 06:02:32 7.874u 0.189s 0:08.91 90.3% 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 06:02:32 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2320 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: 3.258880 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): 25.88100 72.78300 ymin,ymax (A): -18.57800 30.58000 zmin,zma (A): 3.918000 46.56900 x,y,z range (A): 46.90200 49.15800 42.65100 scale (grids/A): 3.258880 object centre (A): 49.33200 6.001000 25.24350 number of atom coordinates read : 2320 total number of charged atoms : 1996 net assigned charge : 6.500008 assigned positive charge : 324.3239 centred at (gu) : 86.24308 92.09741 91.36243 assigned negative charge : -317.8241 centred at (gu) : 86.88525 91.84055 91.73840 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 183402 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17436 grid for indexing accessible points = 1.400000 m= 102626 mr = 136906 m= 44403 mr = 86217 m= 13676 mr = 37082 m= 2951 mr = 10821 m= 402 mr = 2201 m= 22 mr = 278 m= 0 mr = 3 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 73974 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 15968 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) : 2.172586 object centre at (A) : 49.33200 6.001000 25.24350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1268639 0.2885133 midg,1,midg; midg,igrid,midg 0.4019244 0.2214905 1,midg,midg; igrid,midg,midg 0.4989018 -0.7184816 gauss-seidel spectral radius is 0.9993088 estimated iterations to convergence 300 setup time was (sec) 1.480000 now iterating at: 06:02:33 rms-change max change #iterations 10.64130 424.2925 at 10iterations 6.314536 119.2822 at 20iterations 3.747356 69.91373 at 30iterations 2.220671 48.47935 at 40iterations 1.313866 25.61418 at 50iterations 0.7749539 13.32898 at 60iterations 0.4569061 8.778107 at 70iterations 0.2698479 4.429962 at 80iterations 0.1589080 2.786507 at 90iterations 9.3400896E-02 1.691692 at 100iterations 5.5181444E-02 0.9646797 at 110iterations 3.2579154E-02 0.5495968 at 120iterations 1.9374521E-02 0.3458052 at 130iterations 1.1623721E-02 0.1934586 at 140iterations 7.1463925E-03 0.1306629 at 150iterations 4.5152935E-03 9.1827393E-02 at 160iterations 2.9876868E-03 5.4260254E-02 at 170iterations 2.1007892E-03 3.7422180E-02 at 180iterations finished qdiffx linear iterations at : 06:02:45 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 2.1007892E-03 3.7422180E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 06:02:45 12.866u 0.219s 0:13.77 94.9% 0+0k 0+0io 0pf+0w