Tue Nov 22 14:11:59 PST 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 Nov 22 2011 at 14:12:04 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6452783 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): -5.340000 34.55700 ymin,ymax (A): -3.536000 49.05700 zmin,zma (A): -24.23000 30.94000 x,y,z range (A): 39.89700 52.59300 55.17000 scale (grids/A): 0.6452783 object centre (A): 14.60850 22.76050 3.355000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 90.62726 92.32104 90.21054 assigned negative charge : -288.8263 centred at (gu) : 90.72224 92.43806 90.14938 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5583 nv = 96 ne = 84 npr = 40213 no. pairs analyzed = 40213 no. exposed pairs = 2473 no. arc points = 17291 no. surface atoms = 843 nbur = 1121 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 280 mr = 3140 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1686 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6532 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6133177E-10 1.1976096E-08 midg,1,midg; midg,igrid,midg 1.0379778E-08 -1.0846676E-08 1,midg,midg; igrid,midg,midg 1.2924633E-08 -4.7720476E-09 gauss-seidel spectral radius is 0.9874993 estimated iterations to convergence 73 setup time was (sec) 0.3500000 now iterating at: 14:12:07 rms-change max change #iterations 0.1332593 22.32962 at 10iterations 1.3372798E-02 2.075504 at 20iterations 1.3519155E-03 0.2037411 at 30iterations 1.3188350E-04 1.9363403E-02 at 40iterations 1.3343059E-05 2.3918152E-03 at 50iterations finished qdiffx linear iterations at : 14:12:16 total time elapsed so far: 3.690000 # loops : 50 mean,max change (kT/e) : 1.3343059E-05 2.3918152E-03 energy calculations done at 3.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.830000 DelPhi exited at 14:12:18 3.831u 0.205s 0:14.56 27.6% 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 Nov 22 2011 at 14:12:18 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.935835 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): -5.340000 34.55700 ymin,ymax (A): -3.536000 49.05700 zmin,zma (A): -24.23000 30.94000 x,y,z range (A): 39.89700 52.59300 55.17000 scale (grids/A): 1.935835 object centre (A): 14.60850 22.76050 3.355000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 91.88175 96.96288 90.63167 assigned negative charge : -288.8263 centred at (gu) : 92.16676 97.31445 90.44828 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59861 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17291 grid for indexing accessible points = 1.400000 m= 21885 mr = 41278 m= 3229 mr = 16623 m= 134 mr = 2106 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 679 time to turn everything in is 0.3100000 number of dielectric boundary points 25065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14448 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) : 0.6452783 object centre at (A) : 14.60850 22.76050 3.355000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1143862E-02 1.6499469E-02 midg,1,midg; midg,igrid,midg 3.4098063E-02 -8.3623929E-03 1,midg,midg; igrid,midg,midg 5.3024613E-03 -5.0003761E-03 gauss-seidel spectral radius is 0.9985995 estimated iterations to convergence 212 setup time was (sec) 0.5500000 now iterating at: 14:12:20 rms-change max change #iterations 3.735502 204.0685 at 10iterations 1.731262 67.91111 at 20iterations 0.8035442 30.80372 at 30iterations 0.3751537 14.88760 at 40iterations 0.1725629 5.977118 at 50iterations 7.9964861E-02 2.661703 at 60iterations 3.7062608E-02 1.232231 at 70iterations 1.7208492E-02 0.6364212 at 80iterations 7.9780128E-03 0.2676919 at 90iterations 3.6967297E-03 0.1394882 at 100iterations 1.7145361E-03 6.8464279E-02 at 110iterations 7.9652987E-04 3.0647278E-02 at 120iterations finished qdiffx linear iterations at : 14:12:43 total time elapsed so far: 8.660000 # loops : 120 mean,max change (kT/e) : 7.9652987E-04 3.0647278E-02 energy calculations done at 8.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.790000 DelPhi exited at 14:12:45 8.795u 0.235s 0:26.61 33.8% 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 Nov 22 2011 at 14:12:46 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.903752 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): -5.340000 34.55700 ymin,ymax (A): -3.536000 49.05700 zmin,zma (A): -24.23000 30.94000 x,y,z range (A): 39.89700 52.59300 55.17000 scale (grids/A): 2.903752 object centre (A): 14.60850 22.76050 3.355000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 92.82268 100.4443 90.94749 assigned negative charge : -288.8263 centred at (gu) : 93.25016 100.9716 90.67242 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 138126 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17291 grid for indexing accessible points = 1.400000 m= 70391 mr = 99583 m= 25949 mr = 58538 m= 5889 mr = 21522 m= 650 mr = 4530 m= 27 mr = 422 m= 0 mr = 5 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 2281 time to turn everything in is 0.8400000 number of dielectric boundary points 56432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 14656 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) : 1.935835 object centre at (A) : 14.60850 22.76050 3.355000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.145813 5.9048083E-02 midg,1,midg; midg,igrid,midg 0.3607893 -0.1217118 1,midg,midg; igrid,midg,midg 3.1520352E-02 -3.2452121E-02 gauss-seidel spectral radius is 0.9992351 estimated iterations to convergence 285 setup time was (sec) 1.130000 now iterating at: 14:12:53 rms-change max change #iterations 8.759670 514.5583 at 10iterations 5.046626 127.3432 at 20iterations 2.876296 83.75800 at 30iterations 1.644370 52.17460 at 40iterations 0.9380574 25.99925 at 50iterations 0.5341303 14.12291 at 60iterations 0.3050682 6.644272 at 70iterations 0.1733939 3.541496 at 80iterations 9.8849781E-02 2.043733 at 90iterations 5.6067884E-02 1.140522 at 100iterations 3.1952199E-02 0.5937623 at 110iterations 1.8153356E-02 0.4853001 at 120iterations 1.0292180E-02 0.1977005 at 130iterations 5.8601201E-03 0.1237521 at 140iterations 3.3250093E-03 6.4552307E-02 at 150iterations 1.8915969E-03 3.6372185E-02 at 160iterations 1.0738516E-03 2.2216797E-02 at 170iterations 6.1107340E-04 1.2237549E-02 at 180iterations finished qdiffx linear iterations at : 14:13:35 total time elapsed so far: 14.75000 # loops : 180 mean,max change (kT/e) : 6.1107340E-04 1.2237549E-02 energy calculations done at 14.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.85000 DelPhi exited at 14:13:42 14.853u 0.303s 0:56.06 27.0% 0+0k 0+0io 0pf+0w