Sun Feb 12 05:03:06 PST 2012 #!/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_thin.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 Sun Feb 12 2012 at 05:03:06 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 = 2134 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: 0.5708055 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): -32.49700 14.14200 ymin,ymax (A): -26.16100 13.44700 zmin,zma (A): 17.86100 80.22900 x,y,z range (A): 46.63900 39.60800 62.36800 scale (grids/A): 0.5708055 object centre (A): -9.177502 -6.357000 49.04500 number of atom coordinates read : 2134 total number of charged atoms : 1927 net assigned charge : -1.999997 assigned positive charge : 271.8722 centred at (gu) : 91.99503 88.65961 88.47491 assigned negative charge : -273.8725 centred at (gu) : 91.99344 88.66325 88.66789 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4539 nv = 96 ne = 84 npr = 48654 no. pairs analyzed = 48654 no. exposed pairs = 2738 no. arc points = 19460 no. surface atoms = 933 nbur = 1201 mkacc time = 7.9999998E-02 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 = 1.540000 m= 233 mr = 2180 m= 0 mr = 20 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.1700000 number of dielectric boundary points 2572 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1842 ## 135 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 5612 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2052158E-09 -1.5937788E-09 midg,1,midg; midg,igrid,midg -4.2065462E-10 -2.7916472E-10 1,midg,midg; igrid,midg,midg -2.2794613E-10 -5.2343191E-10 gauss-seidel spectral radius is 0.9840999 estimated iterations to convergence 65 setup time was (sec) 0.3700000 now iterating at: 05:03:07 rms-change max change #iterations 6.8226822E-02 13.92478 at 10iterations 5.9533725E-03 1.087073 at 20iterations 1.3374574E-03 0.2759361 at 30iterations 5.6084513E-04 0.1174088 at 40iterations 2.4420695E-04 5.1170349E-02 at 50iterations finished qdiffx linear iterations at : 05:03:10 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 2.4420695E-04 5.1170349E-02 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 05:03:11 3.595u 0.203s 0:04.11 92.2% 0+0k 0+0io 6pf+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 Feb 12 2012 at 05:03:11 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 = 2134 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: 1.712417 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): -32.49700 14.14200 ymin,ymax (A): -26.16100 13.44700 zmin,zma (A): 17.86100 80.22900 x,y,z range (A): 46.63900 39.60800 62.36800 scale (grids/A): 1.712417 object centre (A): -9.177502 -6.357000 49.04500 number of atom coordinates read : 2134 total number of charged atoms : 1927 net assigned charge : -1.999997 assigned positive charge : 271.8722 centred at (gu) : 95.98523 85.97900 85.42516 assigned negative charge : -273.8725 centred at (gu) : 95.98069 85.99010 86.00386 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 49611 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19460 grid for indexing accessible points = 1.400000 m= 15447 mr = 32024 m= 1980 mr = 10337 m= 44 mr = 1054 m= 0 mr = 3 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 842 time to turn everything in is 0.2600000 number of dielectric boundary points 23664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 14997 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) : 0.5708055 object centre at (A) : -9.177502 -6.357000 49.04500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6498880E-02 -1.1724582E-02 midg,1,midg; midg,igrid,midg -3.0522377E-03 -1.0198752E-03 1,midg,midg; igrid,midg,midg -2.4292921E-04 -6.7527586E-04 gauss-seidel spectral radius is 0.9982634 estimated iterations to convergence 191 setup time was (sec) 0.4900000 now iterating at: 05:03:11 rms-change max change #iterations 2.770874 177.1397 at 10iterations 1.175253 55.09363 at 20iterations 0.4965167 22.23543 at 30iterations 0.2121234 8.743431 at 40iterations 9.0410344E-02 3.665027 at 50iterations 3.8779598E-02 1.574036 at 60iterations 1.6759666E-02 0.6592484 at 70iterations 7.6912940E-03 0.3097820 at 80iterations 3.9121299E-03 0.1969547 at 90iterations 2.3300580E-03 0.1094437 at 100iterations 1.5975959E-03 7.1708679E-02 at 110iterations 1.1763403E-03 5.1017761E-02 at 120iterations finished qdiffx linear iterations at : 05:03:19 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 1.1763403E-03 5.1017761E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 05:03:19 8.041u 0.216s 0:08.53 96.7% 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 Sun Feb 12 2012 at 05:03:19 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 = 2134 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: 2.568625 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): -32.49700 14.14200 ymin,ymax (A): -26.16100 13.44700 zmin,zma (A): 17.86100 80.22900 x,y,z range (A): 46.63900 39.60800 62.36800 scale (grids/A): 2.568625 object centre (A): -9.177502 -6.357000 49.04500 number of atom coordinates read : 2134 total number of charged atoms : 1927 net assigned charge : -1.999997 assigned positive charge : 271.8722 centred at (gu) : 98.97779 83.96842 83.13780 assigned negative charge : -273.8725 centred at (gu) : 98.97121 83.98528 84.00581 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 115148 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19460 grid for indexing accessible points = 1.400000 m= 51481 mr = 79102 m= 16460 mr = 39434 m= 3166 mr = 12236 m= 249 mr = 2211 m= 2 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 3014 time to turn everything in is 0.6400000 number of dielectric boundary points 53390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15408 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) : 1.712417 object centre at (A) : -9.177502 -6.357000 49.04500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3188834 -0.1635469 midg,1,midg; midg,igrid,midg -4.3556415E-02 -4.5970115E-03 1,midg,midg; igrid,midg,midg -3.3387074E-03 -1.5023145E-02 gauss-seidel spectral radius is 0.9991386 estimated iterations to convergence 269 setup time was (sec) 0.8900000 now iterating at: 05:03:20 rms-change max change #iterations 7.027042 337.9786 at 10iterations 3.950456 115.1452 at 20iterations 2.199934 58.85442 at 30iterations 1.225114 32.28066 at 40iterations 0.6827947 16.84668 at 50iterations 0.3774407 9.407066 at 60iterations 0.2092754 5.764202 at 70iterations 0.1154505 2.696716 at 80iterations 6.3715652E-02 1.778217 at 90iterations 3.5226606E-02 0.8131189 at 100iterations 1.9422062E-02 0.4544163 at 110iterations 1.0777425E-02 0.2450647 at 120iterations 6.0395235E-03 0.1535873 at 130iterations 3.4401310E-03 8.7234497E-02 at 140iterations 2.0415969E-03 4.9856186E-02 at 150iterations 1.2939627E-03 3.8673401E-02 at 160iterations 8.9958985E-04 2.6535034E-02 at 170iterations 6.8188924E-04 1.8014908E-02 at 180iterations finished qdiffx linear iterations at : 05:03:32 total time elapsed so far: 12.65000 # loops : 180 mean,max change (kT/e) : 6.8188924E-04 1.8014908E-02 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 05:03:32 12.784u 0.229s 0:13.29 97.8% 0+0k 0+0io 0pf+0w