Mon Oct 10 00:05:42 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 Mon Oct 10 2011 at 00:05:42 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3097 !!! WARNING: SEP 140 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6280765 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): -34.87500 19.25300 ymin,ymax (A): -13.16200 37.93600 zmin,zma (A): -14.95400 41.72700 x,y,z range (A): 54.12800 51.09800 56.68100 scale (grids/A): 0.6280765 object centre (A): -7.811000 12.38700 13.38650 number of atom coordinates read : 3097 total number of charged atoms : 2953 net assigned charge : 2.025009 assigned positive charge : 468.4750 centred at (gu) : 90.91404 90.39967 91.65205 assigned negative charge : -466.4513 centred at (gu) : 90.87933 90.30695 91.62953 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8157 nv = 96 ne = 84 npr = 61500 no. pairs analyzed = 61500 no. exposed pairs = 4059 no. arc points = 28819 no. surface atoms = 1353 nbur = 1744 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 409 mr = 4287 m= 3 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2300000 number of dielectric boundary points 4257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2895 ## 288 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 10049 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8612263E-10 6.0395764E-09 midg,1,midg; midg,igrid,midg -6.8032064E-09 1.2192865E-08 1,midg,midg; igrid,midg,midg -1.2396383E-09 6.6272969E-09 gauss-seidel spectral radius is 0.9869190 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 00:05:43 rms-change max change #iterations 0.1444434 18.60641 at 10iterations 1.3808522E-02 1.752539 at 20iterations 1.2979815E-03 0.1535978 at 30iterations 1.2787677E-04 1.6910553E-02 at 40iterations 1.2629544E-05 1.6794205E-03 at 50iterations finished qdiffx linear iterations at : 00:05:46 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.2629544E-05 1.6794205E-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) 3.360000 DelPhi exited at 00:05:46 3.363u 0.175s 0:03.82 92.4% 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 Mon Oct 10 2011 at 00:05:46 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3097 !!! WARNING: SEP 140 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.884229 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): -34.87500 19.25300 ymin,ymax (A): -13.16200 37.93600 zmin,zma (A): -14.95400 41.72700 x,y,z range (A): 54.12800 51.09800 56.68100 scale (grids/A): 1.884229 object centre (A): -7.811000 12.38700 13.38650 number of atom coordinates read : 3097 total number of charged atoms : 2953 net assigned charge : 2.025009 assigned positive charge : 468.4750 centred at (gu) : 92.74149 91.19868 94.95531 assigned negative charge : -466.4513 centred at (gu) : 92.63770 90.92091 94.88811 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 88427 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28819 grid for indexing accessible points = 1.400000 m= 29399 mr = 59699 m= 4143 mr = 20845 m= 211 mr = 2352 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1522 time to turn everything in is 0.4100000 number of dielectric boundary points 39242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 23167 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) : 0.6280765 object centre at (A) : -7.811000 12.38700 13.38650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4915342E-02 -1.7396060E-03 midg,1,midg; midg,igrid,midg -1.5140933E-03 1.6861914E-02 1,midg,midg; igrid,midg,midg -1.6762216E-02 5.3515141E-03 gauss-seidel spectral radius is 0.9986659 estimated iterations to convergence 217 setup time was (sec) 0.6100000 now iterating at: 00:05:47 rms-change max change #iterations 4.649372 170.5880 at 10iterations 2.176541 76.40948 at 20iterations 1.027314 30.89346 at 30iterations 0.4853930 14.86850 at 40iterations 0.2290841 6.507942 at 50iterations 0.1081770 3.190399 at 60iterations 5.0916947E-02 1.453522 at 70iterations 2.4076641E-02 0.7098370 at 80iterations 1.1348567E-02 0.3228760 at 90iterations 5.3639486E-03 0.1692200 at 100iterations 2.5375716E-03 7.2249413E-02 at 110iterations 1.1972518E-03 3.7895679E-02 at 120iterations finished qdiffx linear iterations at : 00:05:54 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.1972518E-03 3.7895679E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 00:05:54 7.777u 0.204s 0:08.27 96.3% 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 Mon Oct 10 2011 at 00:05:55 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3097 !!! WARNING: SEP 140 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.826344 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): -34.87500 19.25300 ymin,ymax (A): -13.16200 37.93600 zmin,zma (A): -14.95400 41.72700 x,y,z range (A): 54.12800 51.09800 56.68100 scale (grids/A): 2.826344 object centre (A): -7.811000 12.38700 13.38650 number of atom coordinates read : 3097 total number of charged atoms : 2953 net assigned charge : 2.025009 assigned positive charge : 468.4750 centred at (gu) : 94.11202 91.79776 97.43301 assigned negative charge : -466.4513 centred at (gu) : 93.95667 91.38111 97.33203 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 204547 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28819 grid for indexing accessible points = 1.400000 m= 97162 mr = 145287 m= 32224 mr = 77833 m= 7193 mr = 25064 m= 915 mr = 5052 m= 44 mr = 543 m= 0 mr = 2 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 5203 time to turn everything in is 1.060000 number of dielectric boundary points 88304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 23617 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) : 1.884229 object centre at (A) : -7.811000 12.38700 13.38650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1796372 -9.0440981E-02 midg,1,midg; midg,igrid,midg 5.9977233E-02 -7.4393883E-02 1,midg,midg; igrid,midg,midg -0.2850312 -3.7307825E-02 gauss-seidel spectral radius is 0.9992912 estimated iterations to convergence 296 setup time was (sec) 1.310000 now iterating at: 00:05:56 rms-change max change #iterations 11.15269 332.1792 at 10iterations 6.691567 169.0088 at 20iterations 3.981563 81.52169 at 30iterations 2.353201 49.43312 at 40iterations 1.386451 25.42027 at 50iterations 0.8141874 15.04626 at 60iterations 0.4768671 8.272745 at 70iterations 0.2795241 4.748562 at 80iterations 0.1630433 2.816620 at 90iterations 9.5216855E-02 1.726902 at 100iterations 5.5406556E-02 0.9228468 at 110iterations 3.2298997E-02 0.5479345 at 120iterations 1.8830094E-02 0.3126268 at 130iterations 1.0964229E-02 0.1759593 at 140iterations 6.3867224E-03 0.1176958 at 150iterations 3.7142653E-03 5.9782982E-02 at 160iterations 2.1605361E-03 3.8653374E-02 at 170iterations 1.2573571E-03 2.2467971E-02 at 180iterations finished qdiffx linear iterations at : 00:06:08 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 1.2573571E-03 2.2467971E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 00:06:08 12.915u 0.189s 0:13.37 97.9% 0+0k 0+0io 0pf+0w