Sat Oct 8 11:39:14 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 11:39:14 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 = 4473 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5497984 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): -27.75400 35.35700 ymin,ymax (A): 34.63100 99.38200 zmin,zma (A): 30.77000 88.93700 x,y,z range (A): 63.11100 64.75101 58.16701 scale (grids/A): 0.5497984 object centre (A): 3.801499 67.00650 59.85350 number of atom coordinates read : 4473 total number of charged atoms : 4313 net assigned charge : -5.499951 assigned positive charge : 671.9590 centred at (gu) : 90.95484 88.28343 89.16039 assigned negative charge : -677.4622 centred at (gu) : 90.82330 88.37608 89.31827 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8515 nv = 96 ne = 84 npr = 94298 no. pairs analyzed = 94298 no. exposed pairs = 4959 no. arc points = 33783 no. surface atoms = 1692 nbur = 2781 mkacc time = 0.1500000 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= 300 mr = 4896 m= 0 mr = 20 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 70 time to turn everything in is 0.2900000 number of dielectric boundary points 3899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3505 ## 444 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 11445 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6746809E-09 -1.8834851E-09 midg,1,midg; midg,igrid,midg 9.6551034E-10 -1.0088997E-09 1,midg,midg; igrid,midg,midg -1.5808340E-09 1.3497778E-09 gauss-seidel spectral radius is 0.9830433 estimated iterations to convergence 63 setup time was (sec) 0.5000000 now iterating at: 11:39:15 rms-change max change #iterations 9.5027275E-02 13.51508 at 10iterations 6.8365000E-03 1.187393 at 20iterations 6.3656608E-04 0.1012192 at 30iterations 1.3482175E-04 2.0318985E-02 at 40iterations 4.4269636E-05 6.8031549E-03 at 50iterations finished qdiffx linear iterations at : 11:39:18 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 4.4269636E-05 6.8031549E-03 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 11:39:18 3.703u 0.210s 0:04.24 92.2% 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 11:39:18 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 = 4473 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.649395 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): -27.75400 35.35700 ymin,ymax (A): 34.63100 99.38200 zmin,zma (A): 30.77000 88.93700 x,y,z range (A): 63.11100 64.75101 58.16701 scale (grids/A): 1.649395 object centre (A): 3.801499 67.00650 59.85350 number of atom coordinates read : 4473 total number of charged atoms : 4313 net assigned charge : -5.499951 assigned positive charge : 671.9590 centred at (gu) : 92.86309 84.84901 87.47957 assigned negative charge : -677.4622 centred at (gu) : 92.46951 85.12784 87.95412 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 96908 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33783 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30971 mr = 70467 m= 3361 mr = 22663 m= 86 mr = 1882 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 6364 time to turn everything in is 0.4800000 number of dielectric boundary points 36305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 367 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 33085 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) : 0.5497984 object centre at (A) : 3.801499 67.00650 59.85350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0663654E-02 -2.1174554E-02 midg,1,midg; midg,igrid,midg 1.9069662E-02 -3.4939344E-03 1,midg,midg; igrid,midg,midg -2.5369775E-02 2.5302608E-02 gauss-seidel spectral radius is 0.9983519 estimated iterations to convergence 196 setup time was (sec) 0.7200000 now iterating at: 11:39:19 rms-change max change #iterations 4.291371 178.5982 at 10iterations 1.867523 55.73785 at 20iterations 0.8163140 25.04406 at 30iterations 0.3560696 9.797005 at 40iterations 0.1553765 4.461963 at 50iterations 6.7493655E-02 2.235214 at 60iterations 2.9440021E-02 0.8583260 at 70iterations 1.2831351E-02 0.4044914 at 80iterations 5.5991113E-03 0.1748390 at 90iterations 2.4632856E-03 7.3101044E-02 at 100iterations 1.0904376E-03 3.2318473E-02 at 110iterations 4.9154722E-04 1.4215946E-02 at 120iterations finished qdiffx linear iterations at : 11:39:27 total time elapsed so far: 8.350000 # loops : 120 mean,max change (kT/e) : 4.9154722E-04 1.4215946E-02 energy calculations done at 8.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.470000 DelPhi exited at 11:39:27 8.472u 0.236s 0:09.05 96.1% 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 8 2011 at 11:39:28 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 = 4473 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.474093 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): -27.75400 35.35700 ymin,ymax (A): 34.63100 99.38200 zmin,zma (A): 30.77000 88.93700 x,y,z range (A): 63.11100 64.75101 58.16701 scale (grids/A): 2.474093 object centre (A): 3.801499 67.00650 59.85350 number of atom coordinates read : 4473 total number of charged atoms : 4313 net assigned charge : -5.499951 assigned positive charge : 671.9590 centred at (gu) : 94.29440 82.27298 86.21899 assigned negative charge : -677.4622 centred at (gu) : 93.70407 82.69164 86.93111 start vw surface at 0.1200000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 225748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33783 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 108176 mr = 171369 m= 31125 mr = 88776 m= 5448 mr = 24544 m= 399 mr = 3946 m= 7 mr = 218 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 21724 time to turn everything in is 1.160000 number of dielectric boundary points 82050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 34461 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) : 1.649395 object centre at (A) : 3.801499 67.00650 59.85350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3828646 -0.2675281 midg,1,midg; midg,igrid,midg 0.3479636 9.3507648E-02 1,midg,midg; igrid,midg,midg -0.3586086 0.3139295 gauss-seidel spectral radius is 0.9992055 estimated iterations to convergence 280 setup time was (sec) 1.410000 now iterating at: 11:39:29 rms-change max change #iterations 10.87790 295.5757 at 10iterations 6.213295 120.9346 at 20iterations 3.555490 74.39398 at 30iterations 2.023393 43.87229 at 40iterations 1.149829 21.46398 at 50iterations 0.6519246 11.11096 at 60iterations 0.3685028 6.815194 at 70iterations 0.2087168 3.592880 at 80iterations 0.1176650 2.038603 at 90iterations 6.6566780E-02 1.159903 at 100iterations 3.7541773E-02 0.6967208 at 110iterations 2.1229435E-02 0.3470564 at 120iterations 1.1976817E-02 0.1999278 at 130iterations 6.7719948E-03 0.1153142 at 140iterations 3.8309526E-03 6.3340187E-02 at 150iterations 2.1759521E-03 3.6158085E-02 at 160iterations 1.2444115E-03 2.0582199E-02 at 170iterations 7.2043558E-04 1.3412476E-02 at 180iterations finished qdiffx linear iterations at : 11:39:41 total time elapsed so far: 13.58000 # loops : 180 mean,max change (kT/e) : 7.2043558E-04 1.3412476E-02 energy calculations done at 13.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.71000 DelPhi exited at 11:39:42 13.712u 0.255s 0:14.26 97.8% 0+0k 0+0io 0pf+0w