Sat Oct 8 23:30:31 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 8 2011 at 23:30:31 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 = 2522 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: 0.6020225 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): -32.46400 26.67000 ymin,ymax (A): 8.249000 49.89900 zmin,zma (A): -11.45700 43.35800 x,y,z range (A): 59.13400 41.65000 54.81500 scale (grids/A): 0.6020225 object centre (A): -2.897000 29.07400 15.95050 number of atom coordinates read : 2522 total number of charged atoms : 2385 net assigned charge : 9.500029 assigned positive charge : 369.1182 centred at (gu) : 91.43823 90.97905 90.54247 assigned negative charge : -359.6189 centred at (gu) : 91.36431 90.87964 90.47614 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6100 nv = 96 ne = 84 npr = 50518 no. pairs analyzed = 50518 no. exposed pairs = 3329 no. arc points = 23735 no. surface atoms = 1113 nbur = 1409 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 282 mr = 3119 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3244 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2334 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7612 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6479788E-09 7.4518605E-09 midg,1,midg; midg,igrid,midg 5.4282101E-10 9.6818225E-09 1,midg,midg; igrid,midg,midg 1.1775259E-09 9.4942578E-09 gauss-seidel spectral radius is 0.9857178 estimated iterations to convergence 69 setup time was (sec) 0.4100000 now iterating at: 23:30:31 rms-change max change #iterations 0.1013393 16.16620 at 10iterations 8.7952614E-03 1.576337 at 20iterations 7.5717934E-04 0.1142856 at 30iterations 7.2066810E-05 1.0869980E-02 at 40iterations 8.7420322E-06 1.4462471E-03 at 50iterations finished qdiffx linear iterations at : 23:30:35 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 8.7420322E-06 1.4462471E-03 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 23:30:35 3.684u 0.209s 0:04.19 92.6% 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 Sat Oct 8 2011 at 23:30:35 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 = 2522 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: 1.806067 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): -32.46400 26.67000 ymin,ymax (A): 8.249000 49.89900 zmin,zma (A): -11.45700 43.35800 x,y,z range (A): 59.13400 41.65000 54.81500 scale (grids/A): 1.806067 object centre (A): -2.897000 29.07400 15.95050 number of atom coordinates read : 2522 total number of charged atoms : 2385 net assigned charge : 9.500029 assigned positive charge : 369.1182 centred at (gu) : 94.31422 92.93679 91.62702 assigned negative charge : -359.6189 centred at (gu) : 94.09277 92.63872 91.42847 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65796 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23735 grid for indexing accessible points = 1.400000 m= 21900 mr = 43748 m= 3087 mr = 15416 m= 168 mr = 1789 m= 4 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 831 time to turn everything in is 0.3400000 number of dielectric boundary points 29949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 221 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18611 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) : 0.6020225 object centre at (A) : -2.897000 29.07400 15.95050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2162212E-02 2.5098410E-02 midg,1,midg; midg,igrid,midg -3.8306214E-04 1.9601462E-02 1,midg,midg; igrid,midg,midg -8.3187558E-03 4.8405845E-02 gauss-seidel spectral radius is 0.9984822 estimated iterations to convergence 204 setup time was (sec) 0.6100000 now iterating at: 23:30:36 rms-change max change #iterations 3.650340 182.4354 at 10iterations 1.626175 65.40369 at 20iterations 0.7305967 25.00992 at 30iterations 0.3283313 10.84848 at 40iterations 0.1467831 5.216149 at 50iterations 6.5904781E-02 2.369476 at 60iterations 2.9668108E-02 0.9697564 at 70iterations 1.3283269E-02 0.4856057 at 80iterations 5.9598838E-03 0.1969118 at 90iterations 2.6828544E-03 9.1480255E-02 at 100iterations 1.2061340E-03 4.3883324E-02 at 110iterations 5.4228393E-04 1.8030167E-02 at 120iterations finished qdiffx linear iterations at : 23:30:44 total time elapsed so far: 8.790000 # loops : 120 mean,max change (kT/e) : 5.4228393E-04 1.8030167E-02 energy calculations done at 8.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.930000 DelPhi exited at 23:30:45 8.933u 0.266s 0:09.53 96.4% 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 Sat Oct 8 2011 at 23:30:45 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 = 2522 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: 2.709101 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): -32.46400 26.67000 ymin,ymax (A): 8.249000 49.89900 zmin,zma (A): -11.45700 43.35800 x,y,z range (A): 59.13400 41.65000 54.81500 scale (grids/A): 2.709101 object centre (A): -2.897000 29.07400 15.95050 number of atom coordinates read : 2522 total number of charged atoms : 2385 net assigned charge : 9.500029 assigned positive charge : 369.1182 centred at (gu) : 96.47127 94.40506 92.44052 assigned negative charge : -359.6189 centred at (gu) : 96.13918 93.95816 92.14268 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 152447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23735 grid for indexing accessible points = 1.400000 m= 72129 mr = 107027 m= 24111 mr = 56983 m= 5344 mr = 18807 m= 687 mr = 3917 m= 35 mr = 436 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 2958 time to turn everything in is 0.8600000 number of dielectric boundary points 67570 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 19077 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) : 1.806067 object centre at (A) : -2.897000 29.07400 15.95050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5214679 0.2778817 midg,1,midg; midg,igrid,midg 1.9005337E-03 0.2080740 1,midg,midg; igrid,midg,midg -0.1247632 0.5372347 gauss-seidel spectral radius is 0.9992236 estimated iterations to convergence 283 setup time was (sec) 1.140000 now iterating at: 23:30:46 rms-change max change #iterations 8.917410 262.6386 at 10iterations 5.178519 133.8689 at 20iterations 2.984623 96.02678 at 30iterations 1.713287 42.72011 at 40iterations 0.9844585 24.41227 at 50iterations 0.5608745 12.28721 at 60iterations 0.3206332 6.637123 at 70iterations 0.1827321 3.952175 at 80iterations 0.1039453 2.093309 at 90iterations 5.9037793E-02 1.221181 at 100iterations 3.3590011E-02 0.6692410 at 110iterations 1.9097729E-02 0.3955128 at 120iterations 1.0814929E-02 0.2210267 at 130iterations 6.1416621E-03 0.1364441 at 140iterations 3.4943670E-03 7.0388794E-02 at 150iterations 1.9774677E-03 3.7355423E-02 at 160iterations 1.1224460E-03 1.9701481E-02 at 170iterations 6.3581835E-04 1.2887955E-02 at 180iterations finished qdiffx linear iterations at : 23:30:59 total time elapsed so far: 14.03000 # loops : 180 mean,max change (kT/e) : 6.3581835E-04 1.2887955E-02 energy calculations done at 14.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.17000 DelPhi exited at 23:30:59 14.167u 0.283s 0:14.72 98.0% 0+0k 0+0io 0pf+0w