Sat Oct 15 13:53:11 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 Sat Oct 15 2011 at 13:53:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 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: 0.5862881 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): -8.375999 49.72100 ymin,ymax (A): -7.280000 44.40000 zmin,zma (A): 27.29300 88.01400 x,y,z range (A): 58.09700 51.68000 60.72100 scale (grids/A): 0.5862881 object centre (A): 20.67250 18.56000 57.65350 number of atom coordinates read : 2623 total number of charged atoms : 2489 net assigned charge : 12.00001 assigned positive charge : 383.7747 centred at (gu) : 89.35731 90.82004 91.52212 assigned negative charge : -371.7755 centred at (gu) : 89.26685 90.71681 91.52288 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6098 nv = 96 ne = 84 npr = 52923 no. pairs analyzed = 52923 no. exposed pairs = 3341 no. arc points = 23797 no. surface atoms = 1128 nbur = 1495 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 297 mr = 3172 m= 0 mr = 20 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3203 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2431 ## 292 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7612 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3218096E-09 4.5483310E-09 midg,1,midg; midg,igrid,midg 7.5482981E-10 6.6914589E-09 1,midg,midg; igrid,midg,midg 1.3434018E-09 4.5417683E-09 gauss-seidel spectral radius is 0.9849585 estimated iterations to convergence 67 setup time was (sec) 0.4800000 now iterating at: 13:53:12 rms-change max change #iterations 9.4831094E-02 18.15903 at 10iterations 7.5494223E-03 1.340439 at 20iterations 5.9448340E-04 0.1107111 at 30iterations 4.8723301E-05 7.0991516E-03 at 40iterations 4.3386131E-06 6.8664551E-04 at 50iterations finished qdiffx linear iterations at : 13:53:15 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 4.3386131E-06 6.8664551E-04 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 13:53:15 3.108u 0.164s 0:03.56 91.5% 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 Sat Oct 15 2011 at 13:53:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 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: 1.758864 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): -8.375999 49.72100 ymin,ymax (A): -7.280000 44.40000 zmin,zma (A): 27.29300 88.01400 x,y,z range (A): 58.09700 51.68000 60.72100 scale (grids/A): 1.758864 object centre (A): 20.67250 18.56000 57.65350 number of atom coordinates read : 2623 total number of charged atoms : 2489 net assigned charge : 12.00001 assigned positive charge : 383.7747 centred at (gu) : 88.07114 92.45940 94.56586 assigned negative charge : -371.7755 centred at (gu) : 87.80041 92.15009 94.56850 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 66391 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23797 grid for indexing accessible points = 1.400000 m= 21954 mr = 44948 m= 2971 mr = 15465 m= 141 mr = 1541 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 808 time to turn everything in is 0.4700000 number of dielectric boundary points 29473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 225 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 19372 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) : 0.5862881 object centre at (A) : 20.67250 18.56000 57.65350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1926025E-03 8.7637724E-03 midg,1,midg; midg,igrid,midg 1.3172324E-02 3.8782138E-02 1,midg,midg; igrid,midg,midg -3.5654828E-03 4.6962840E-03 gauss-seidel spectral radius is 0.9984095 estimated iterations to convergence 199 setup time was (sec) 0.7400000 now iterating at: 13:53:16 rms-change max change #iterations 3.522052 180.2980 at 10iterations 1.543970 62.34575 at 20iterations 0.6808276 26.12999 at 30iterations 0.3000221 10.05928 at 40iterations 0.1318276 4.737054 at 50iterations 5.8070038E-02 2.038199 at 60iterations 2.5680153E-02 0.9766846 at 70iterations 1.1298435E-02 0.4426880 at 80iterations 4.9754786E-03 0.1592121 at 90iterations 2.2045218E-03 7.5252533E-02 at 100iterations 9.7381091E-04 3.4801483E-02 at 110iterations 4.2852043E-04 1.7956257E-02 at 120iterations finished qdiffx linear iterations at : 13:53:22 total time elapsed so far: 6.900000 # loops : 120 mean,max change (kT/e) : 4.2852043E-04 1.7956257E-02 energy calculations done at 6.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 13:53:23 7.072u 0.176s 0:07.64 94.7% 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 Sat Oct 15 2011 at 13:53:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 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: 2.638296 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): -8.375999 49.72100 ymin,ymax (A): -7.280000 44.40000 zmin,zma (A): 27.29300 88.01400 x,y,z range (A): 58.09700 51.68000 60.72100 scale (grids/A): 2.638296 object centre (A): 20.67250 18.56000 57.65350 number of atom coordinates read : 2623 total number of charged atoms : 2489 net assigned charge : 12.00001 assigned positive charge : 383.7747 centred at (gu) : 87.10656 93.68878 96.84853 assigned negative charge : -371.7755 centred at (gu) : 86.70063 93.22504 96.85273 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 154230 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23797 grid for indexing accessible points = 1.400000 m= 73705 mr = 110061 m= 24020 mr = 58880 m= 4900 mr = 18248 m= 568 mr = 3324 m= 18 mr = 299 m= 0 mr = 3 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 2726 time to turn everything in is 1.140000 number of dielectric boundary points 66626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 19902 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) : 1.758864 object centre at (A) : 20.67250 18.56000 57.65350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3175780E-02 0.2199364 midg,1,midg; midg,igrid,midg 9.0842545E-02 0.4939840 1,midg,midg; igrid,midg,midg 8.4368750E-02 6.8636276E-02 gauss-seidel spectral radius is 0.9992006 estimated iterations to convergence 279 setup time was (sec) 1.420000 now iterating at: 13:53:24 rms-change max change #iterations 8.769716 310.2508 at 10iterations 5.041214 135.5239 at 20iterations 2.887236 72.59389 at 30iterations 1.635006 42.35168 at 40iterations 0.9279357 21.74314 at 50iterations 0.5245300 11.85161 at 60iterations 0.2959093 5.800313 at 70iterations 0.1669177 3.300581 at 80iterations 9.3827568E-02 2.019780 at 90iterations 5.2954689E-02 1.071171 at 100iterations 2.9764174E-02 0.7630997 at 110iterations 1.6754897E-02 0.3567924 at 120iterations 9.4453562E-03 0.1982975 at 130iterations 5.3093969E-03 0.1097960 at 140iterations 2.9994305E-03 5.9818268E-02 at 150iterations 1.6928300E-03 3.6895752E-02 at 160iterations 9.5815916E-04 2.1859765E-02 at 170iterations 5.4891419E-04 1.4106750E-02 at 180iterations finished qdiffx linear iterations at : 13:53:34 total time elapsed so far: 10.91000 # loops : 180 mean,max change (kT/e) : 5.4891419E-04 1.4106750E-02 energy calculations done at 10.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.09000 DelPhi exited at 13:53:34 11.088u 0.184s 0:11.61 96.9% 0+0k 0+0io 0pf+0w