Mon Oct 10 09:21:42 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 09:21:43 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.6474022 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): -34.40000 5.499000 ymin,ymax (A): -4.919000 46.39400 zmin,zma (A): -31.24400 23.74500 x,y,z range (A): 39.89900 51.31300 54.98900 scale (grids/A): 0.6474022 object centre (A): -14.45050 20.73750 -3.749500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 90.62403 87.39330 90.09853 assigned negative charge : -286.4003 centred at (gu) : 90.72537 87.27661 90.16475 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5649 nv = 96 ne = 84 npr = 40495 no. pairs analyzed = 40495 no. exposed pairs = 2502 no. arc points = 17359 no. surface atoms = 842 nbur = 1128 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 283 mr = 3107 m= 0 mr = 30 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1796 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6679 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2388542E-08 -1.1757180E-09 midg,1,midg; midg,igrid,midg -1.1837400E-08 1.0323474E-08 1,midg,midg; igrid,midg,midg 1.4234854E-08 -5.6203167E-09 gauss-seidel spectral radius is 0.9875812 estimated iterations to convergence 73 setup time was (sec) 0.5000000 now iterating at: 09:21:43 rms-change max change #iterations 0.1285347 20.91726 at 10iterations 1.2822180E-02 2.175868 at 20iterations 1.3291268E-03 0.2050743 at 30iterations 1.3254852E-04 2.7467728E-02 at 40iterations 1.3806687E-05 2.1972656E-03 at 50iterations finished qdiffx linear iterations at : 09:21:46 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.3806687E-05 2.1972656E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 09:21:46 3.333u 0.137s 0:03.86 89.6% 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 09:21:46 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.942207 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): -34.40000 5.499000 ymin,ymax (A): -4.919000 46.39400 zmin,zma (A): -31.24400 23.74500 x,y,z range (A): 39.89900 51.31300 54.98900 scale (grids/A): 1.942207 object centre (A): -14.45050 20.73750 -3.749500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 91.87212 82.17995 90.29563 assigned negative charge : -286.4003 centred at (gu) : 92.17616 81.83016 90.49439 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 60897 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17359 grid for indexing accessible points = 1.400000 m= 21601 mr = 41952 m= 3100 mr = 16352 m= 142 mr = 1928 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1233 time to turn everything in is 0.4900000 number of dielectric boundary points 25478 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 14493 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) : 0.6474022 object centre at (A) : -14.45050 20.73750 -3.749500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2354479E-02 4.8893198E-02 midg,1,midg; midg,igrid,midg -3.8800456E-03 3.2609131E-02 1,midg,midg; igrid,midg,midg 8.6030746E-03 -5.6467741E-03 gauss-seidel spectral radius is 0.9986086 estimated iterations to convergence 212 setup time was (sec) 0.7900000 now iterating at: 09:21:47 rms-change max change #iterations 3.687737 176.0736 at 10iterations 1.718421 66.00246 at 20iterations 0.7972552 29.30082 at 30iterations 0.3704626 14.48051 at 40iterations 0.1721324 6.262802 at 50iterations 8.0270335E-02 2.746267 at 60iterations 3.7226949E-02 1.360161 at 70iterations 1.7307719E-02 0.5744054 at 80iterations 8.0472678E-03 0.2727280 at 90iterations 3.7372257E-03 0.1323853 at 100iterations 1.7330754E-03 6.7504883E-02 at 110iterations 8.0520049E-04 3.3896208E-02 at 120iterations finished qdiffx linear iterations at : 09:21:54 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 8.0520049E-04 3.3896208E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 09:21:55 8.036u 0.219s 0:08.66 95.1% 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 Mon Oct 10 2011 at 09:21:55 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.913310 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): -34.40000 5.499000 ymin,ymax (A): -4.919000 46.39400 zmin,zma (A): -31.24400 23.74500 x,y,z range (A): 39.89900 51.31300 54.98900 scale (grids/A): 2.913310 object centre (A): -14.45050 20.73750 -3.749500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 92.80818 78.26979 90.44344 assigned negative charge : -286.4003 centred at (gu) : 93.26427 77.74534 90.74156 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 140932 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17359 grid for indexing accessible points = 1.400000 m= 70778 mr = 101803 m= 24828 mr = 58534 m= 5346 mr = 20304 m= 637 mr = 4045 m= 30 mr = 404 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.6700001 no. cavity mid-points inaccessible to solvent = 4220 time to turn everything in is 1.210000 number of dielectric boundary points 57457 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 14704 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) : 1.942207 object centre at (A) : -14.45050 20.73750 -3.749500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1413865E-03 1.013250 midg,1,midg; midg,igrid,midg -9.1543511E-02 0.3558997 1,midg,midg; igrid,midg,midg 5.0304573E-02 -3.6474805E-02 gauss-seidel spectral radius is 0.9992388 estimated iterations to convergence 286 setup time was (sec) 1.550000 now iterating at: 09:21:57 rms-change max change #iterations 8.710352 341.9237 at 10iterations 5.012761 128.0797 at 20iterations 2.864269 63.02789 at 30iterations 1.634185 33.68742 at 40iterations 0.9343622 19.52112 at 50iterations 0.5313950 10.92707 at 60iterations 0.3030727 6.478946 at 70iterations 0.1724566 3.563454 at 80iterations 9.8351575E-02 1.982357 at 90iterations 5.5938754E-02 1.254877 at 100iterations 3.1856935E-02 0.6190739 at 110iterations 1.8112203E-02 0.3594751 at 120iterations 1.0319042E-02 0.2098408 at 130iterations 5.8598071E-03 0.1237335 at 140iterations 3.3377914E-03 6.4453125E-02 at 150iterations 1.8989238E-03 4.6993256E-02 at 160iterations 1.0810426E-03 2.0772934E-02 at 170iterations 6.1393913E-04 1.2720227E-02 at 180iterations finished qdiffx linear iterations at : 09:22:08 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 6.1393913E-04 1.2720227E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 09:22:08 12.770u 0.236s 0:13.29 97.8% 0+0k 0+0io 0pf+0w