Mon Oct 10 13:54:54 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 Mon Oct 10 2011 at 13:54:54 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 = 2411 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: 0.6922837 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): -14.43600 36.98800 ymin,ymax (A): -0.4290000 44.33000 zmin,zma (A): -6.457000 43.87400 x,y,z range (A): 51.42400 44.75900 50.33100 scale (grids/A): 0.6922837 object centre (A): 11.27600 21.95050 18.70850 number of atom coordinates read : 2411 total number of charged atoms : 2269 net assigned charge : 3.500024 assigned positive charge : 369.1930 centred at (gu) : 91.12343 91.42206 89.92096 assigned negative charge : -365.6936 centred at (gu) : 91.31023 91.48405 89.88634 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7594 nv = 96 ne = 84 npr = 48270 no. pairs analyzed = 48270 no. exposed pairs = 3136 no. arc points = 21175 no. surface atoms = 1047 nbur = 1364 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 526 mr = 4146 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1974 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8727 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7924982E-09 3.5430688E-08 midg,1,midg; midg,igrid,midg 3.5579141E-08 -5.3005986E-09 1,midg,midg; igrid,midg,midg 7.7357100E-08 -7.0782413E-08 gauss-seidel spectral radius is 0.9891593 estimated iterations to convergence 78 setup time was (sec) 0.3900000 now iterating at: 13:54:55 rms-change max change #iterations 0.1996036 27.75837 at 10iterations 2.3683446E-02 3.468567 at 20iterations 2.9362349E-03 0.3994406 at 30iterations 4.8941991E-04 7.0209503E-02 at 40iterations 1.2499517E-04 1.7066956E-02 at 50iterations finished qdiffx linear iterations at : 13:54:57 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.2499517E-04 1.7066956E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 13:54:58 3.381u 0.159s 0:04.17 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 Mon Oct 10 2011 at 13:54:58 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 = 2411 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: 2.076851 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): -14.43600 36.98800 ymin,ymax (A): -0.4290000 44.33000 zmin,zma (A): -6.457000 43.87400 x,y,z range (A): 51.42400 44.75900 50.33100 scale (grids/A): 2.076851 object centre (A): 11.27600 21.95050 18.70850 number of atom coordinates read : 2411 total number of charged atoms : 2269 net assigned charge : 3.500024 assigned positive charge : 369.1930 centred at (gu) : 93.36988 94.26568 89.76256 assigned negative charge : -365.6936 centred at (gu) : 93.93056 94.45206 89.65888 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21175 grid for indexing accessible points = 1.400000 m= 31701 mr = 55355 m= 6260 mr = 23541 m= 625 mr = 4189 m= 12 mr = 327 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 0.4200000 number of dielectric boundary points 35605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17992 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) : 0.6922837 object centre at (A) : 11.27600 21.95050 18.70850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2321259E-02 1.4689253E-02 midg,1,midg; midg,igrid,midg 3.2665666E-02 2.9559345E-03 1,midg,midg; igrid,midg,midg 1.8261630E-02 -7.0885636E-02 gauss-seidel spectral radius is 0.9988225 estimated iterations to convergence 231 setup time was (sec) 0.6400000 now iterating at: 13:54:59 rms-change max change #iterations 4.913674 214.5517 at 10iterations 2.423361 93.31979 at 20iterations 1.199253 45.06682 at 30iterations 0.5927900 18.22151 at 40iterations 0.2934312 8.096430 at 50iterations 0.1457056 4.369310 at 60iterations 7.2160132E-02 2.050934 at 70iterations 3.5813268E-02 1.049456 at 80iterations 1.7792143E-02 0.4874029 at 90iterations 8.8708932E-03 0.2433600 at 100iterations 4.4553890E-03 0.1257172 at 110iterations 2.2786055E-03 6.5305531E-02 at 120iterations finished qdiffx linear iterations at : 13:55:06 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 2.2786055E-03 6.5305531E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 13:55:07 7.913u 0.232s 0:08.62 94.4% 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 13:55:09 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 = 2411 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: 3.115277 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): -14.43600 36.98800 ymin,ymax (A): -0.4290000 44.33000 zmin,zma (A): -6.457000 43.87400 x,y,z range (A): 51.42400 44.75900 50.33100 scale (grids/A): 3.115277 object centre (A): 11.27600 21.95050 18.70850 number of atom coordinates read : 2411 total number of charged atoms : 2269 net assigned charge : 3.500024 assigned positive charge : 369.1930 centred at (gu) : 95.05456 96.39831 89.64371 assigned negative charge : -365.6936 centred at (gu) : 95.89578 96.67801 89.48811 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 185245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21175 grid for indexing accessible points = 1.400000 m= 98045 mr = 133625 m= 40591 mr = 80212 m= 11934 mr = 33132 m= 2601 mr = 9285 m= 338 mr = 1955 m= 21 mr = 209 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 80353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 18152 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) : 2.076851 object centre at (A) : 11.27600 21.95050 18.70850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2821748 3.7385691E-02 midg,1,midg; midg,igrid,midg 0.2838028 -0.1025465 1,midg,midg; igrid,midg,midg 0.3605787 -0.6689719 gauss-seidel spectral radius is 0.9992990 estimated iterations to convergence 298 setup time was (sec) 1.500000 now iterating at: 13:55:11 rms-change max change #iterations 11.02045 460.6797 at 10iterations 6.558054 126.7040 at 20iterations 3.878047 79.59764 at 30iterations 2.291160 40.83971 at 40iterations 1.351889 22.76637 at 50iterations 0.7947627 15.96000 at 60iterations 0.4668488 8.368317 at 70iterations 0.2737909 4.447607 at 80iterations 0.1605099 2.843666 at 90iterations 9.4002232E-02 1.618251 at 100iterations 5.5182867E-02 1.020966 at 110iterations 3.2483809E-02 0.5790859 at 120iterations 1.9050783E-02 0.3291359 at 130iterations 1.1326466E-02 0.1978502 at 140iterations 6.7799166E-03 0.1433105 at 150iterations 4.1580005E-03 7.9511642E-02 at 160iterations 2.6475354E-03 5.6039810E-02 at 170iterations 1.7750448E-03 3.9611816E-02 at 180iterations finished qdiffx linear iterations at : 13:55:23 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 1.7750448E-03 3.9611816E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 13:55:23 13.087u 0.222s 0:13.78 96.5% 0+0k 0+0io 0pf+0w