Sat Oct 15 12:33:26 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 Sat Oct 15 2011 at 12:33:26 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2749 !!! WARNING: NAP 319 has a net charge of -2.7230 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: 0.5447423 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): -18.05200 26.16400 ymin,ymax (A): 16.34400 81.69600 zmin,zma (A): -8.601000 46.30700 x,y,z range (A): 44.21600 65.35200 54.90800 scale (grids/A): 0.5447423 object centre (A): 4.056000 49.02000 18.85300 number of atom coordinates read : 2749 total number of charged atoms : 2563 net assigned charge : -16.22298 assigned positive charge : 407.8865 centred at (gu) : 90.45444 89.66559 88.88516 assigned negative charge : -424.1100 centred at (gu) : 90.18203 89.74162 88.73144 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5281 nv = 96 ne = 84 npr = 56718 no. pairs analyzed = 56718 no. exposed pairs = 3682 no. arc points = 25643 no. surface atoms = 1232 nbur = 1517 mkacc time = 0.1600000 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 = 1.568000 m= 174 mr = 2552 m= 0 mr = 8 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 2895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2595 ## 328 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 6822 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5104032E-09 -4.3075602E-11 midg,1,midg; midg,igrid,midg -5.4095317E-10 -1.3087903E-09 1,midg,midg; igrid,midg,midg -2.3772873E-09 7.1808071E-10 gauss-seidel spectral radius is 0.9826115 estimated iterations to convergence 62 setup time was (sec) 0.6700000 now iterating at: 12:33:27 rms-change max change #iterations 6.9555596E-02 12.35448 at 10iterations 4.5197201E-03 0.9090557 at 20iterations 4.0392185E-04 5.5980682E-02 at 30iterations 8.1362981E-05 1.0313034E-02 at 40iterations 2.2465252E-05 2.7008057E-03 at 50iterations finished qdiffx linear iterations at : 12:33:31 total time elapsed so far: 5.020000 # loops : 50 mean,max change (kT/e) : 2.2465252E-05 2.7008057E-03 energy calculations done at 5.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.170000 DelPhi exited at 12:33:32 5.174u 0.472s 0:05.95 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 12:33:32 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2749 !!! WARNING: NAP 319 has a net charge of -2.7230 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: 1.634227 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): -18.05200 26.16400 ymin,ymax (A): 16.34400 81.69600 zmin,zma (A): -8.601000 46.30700 x,y,z range (A): 44.21600 65.35200 54.90800 scale (grids/A): 1.634227 object centre (A): 4.056000 49.02000 18.85300 number of atom coordinates read : 2749 total number of charged atoms : 2563 net assigned charge : -16.22298 assigned positive charge : 407.8865 centred at (gu) : 91.36274 88.99609 86.65510 assigned negative charge : -424.1100 centred at (gu) : 90.54567 89.22472 86.19375 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 58505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25643 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 17109 mr = 38422 m= 1445 mr = 11462 m= 24 mr = 576 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 58 time to turn everything in is 0.5100000 number of dielectric boundary points 26623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 273 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19684 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) : 0.5447423 object centre at (A) : 4.056000 49.02000 18.85300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1856254E-02 -3.4907542E-03 midg,1,midg; midg,igrid,midg -1.6148811E-02 -5.3886648E-02 1,midg,midg; igrid,midg,midg -2.0650042E-02 4.5812880E-03 gauss-seidel spectral radius is 0.9981570 estimated iterations to convergence 185 setup time was (sec) 0.8400000 now iterating at: 12:33:33 rms-change max change #iterations 3.212284 171.9482 at 10iterations 1.333008 55.17025 at 20iterations 0.5521752 21.40732 at 30iterations 0.2279401 9.046990 at 40iterations 9.4479270E-02 3.846848 at 50iterations 3.9137136E-02 1.504347 at 60iterations 1.6193194E-02 0.6709309 at 70iterations 6.7207939E-03 0.2547302 at 80iterations 2.7990539E-03 0.1136074 at 90iterations 1.1803237E-03 4.1205883E-02 at 100iterations 5.0456112E-04 1.7730713E-02 at 110iterations 2.2506769E-04 8.3007813E-03 at 120iterations finished qdiffx linear iterations at : 12:33:44 total time elapsed so far: 12.03000 # loops : 120 mean,max change (kT/e) : 2.2506769E-04 8.3007813E-03 energy calculations done at 12.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 12:33:45 12.196u 0.541s 0:13.11 97.1% 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 12:33:45 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2749 !!! WARNING: NAP 319 has a net charge of -2.7230 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: 2.451340 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): -18.05200 26.16400 ymin,ymax (A): 16.34400 81.69600 zmin,zma (A): -8.601000 46.30700 x,y,z range (A): 44.21600 65.35200 54.90800 scale (grids/A): 2.451340 object centre (A): 4.056000 49.02000 18.85300 number of atom coordinates read : 2749 total number of charged atoms : 2563 net assigned charge : -16.22298 assigned positive charge : 407.8865 centred at (gu) : 92.04395 88.49397 84.98223 assigned negative charge : -424.1100 centred at (gu) : 90.81841 88.83702 84.29053 start vw surface at 0.1100000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 135410 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25643 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 60259 mr = 94011 m= 15790 mr = 46920 m= 2132 mr = 11472 m= 118 mr = 1271 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 283 time to turn everything in is 1.230000 number of dielectric boundary points 59984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 20488 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) : 1.634227 object centre at (A) : 4.056000 49.02000 18.85300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2866240 -4.3250091E-02 midg,1,midg; midg,igrid,midg -0.2164388 -0.7598917 1,midg,midg; igrid,midg,midg -0.2876052 7.7507369E-02 gauss-seidel spectral radius is 0.9991279 estimated iterations to convergence 268 setup time was (sec) 1.620000 now iterating at: 12:33:47 rms-change max change #iterations 8.459788 311.2356 at 10iterations 4.762036 131.2423 at 20iterations 2.674574 68.26863 at 30iterations 1.496123 37.92826 at 40iterations 0.8319240 21.52589 at 50iterations 0.4624200 11.95030 at 60iterations 0.2564017 5.998469 at 70iterations 0.1417770 3.399131 at 80iterations 7.8293934E-02 1.841240 at 90iterations 4.3185011E-02 0.9943008 at 100iterations 2.3786729E-02 0.6081457 at 110iterations 1.3101088E-02 0.3124123 at 120iterations 7.2112754E-03 0.1663632 at 130iterations 3.9713131E-03 0.1119067 at 140iterations 2.1890115E-03 5.5575848E-02 at 150iterations 1.2075198E-03 2.7245522E-02 at 160iterations 6.7040109E-04 1.4515877E-02 at 170iterations 3.7493810E-04 8.8653564E-03 at 180iterations finished qdiffx linear iterations at : 12:34:06 total time elapsed so far: 20.05000 # loops : 180 mean,max change (kT/e) : 3.7493810E-04 8.8653564E-03 energy calculations done at 20.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.22000 DelPhi exited at 12:34:06 20.225u 0.551s 0:21.08 98.5% 0+0k 0+0io 0pf+0w