Mon Oct 10 23:52:53 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 Mon Oct 10 2011 at 23:52:53 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2631 !!! WARNING: SEP 216 has a net charge of -0.4750 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 0.5844689 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): 10.40200 64.78800 ymin,ymax (A): -1.271000 59.63900 zmin,zma (A): 10.34000 54.00600 x,y,z range (A): 54.38600 60.91000 43.66600 scale (grids/A): 0.5844689 object centre (A): 37.59500 29.18400 32.17300 number of atom coordinates read : 2631 total number of charged atoms : 2485 net assigned charge : 8.431020 assigned positive charge : 397.6408 centred at (gu) : 88.66154 90.59444 89.60066 assigned negative charge : -389.2104 centred at (gu) : 88.66492 90.48583 89.72084 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5828 nv = 96 ne = 84 npr = 52935 no. pairs analyzed = 52935 no. exposed pairs = 3175 no. arc points = 21928 no. surface atoms = 1063 nbur = 1568 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 = 1.484000 m= 254 mr = 3216 m= 0 mr = 13 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.3600000 number of dielectric boundary points 2853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2216 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7418 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2217124E-09 -5.3503835E-10 midg,1,midg; midg,igrid,midg -2.7651362E-10 5.1753628E-09 1,midg,midg; igrid,midg,midg 2.9735574E-09 1.5167507E-09 gauss-seidel spectral radius is 0.9848551 estimated iterations to convergence 67 setup time was (sec) 0.6700000 now iterating at: 23:52:54 rms-change max change #iterations 9.8553076E-02 17.72022 at 10iterations 8.8037299E-03 1.529774 at 20iterations 1.1900093E-03 0.2698021 at 30iterations 2.9335305E-04 7.3680878E-02 at 40iterations 8.0154692E-05 2.0389557E-02 at 50iterations finished qdiffx linear iterations at : 23:52:57 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 8.0154692E-05 2.0389557E-02 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 23:52:58 4.239u 0.231s 0:04.96 89.9% 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 23:52:58 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2631 !!! WARNING: SEP 216 has a net charge of -0.4750 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 1.753407 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): 10.40200 64.78800 ymin,ymax (A): -1.271000 59.63900 zmin,zma (A): 10.34000 54.00600 x,y,z range (A): 54.38600 60.91000 43.66600 scale (grids/A): 1.753407 object centre (A): 37.59500 29.18400 32.17300 number of atom coordinates read : 2631 total number of charged atoms : 2485 net assigned charge : 8.431020 assigned positive charge : 397.6408 centred at (gu) : 85.98396 91.78285 88.80155 assigned negative charge : -389.2104 centred at (gu) : 85.99432 91.45707 89.16208 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 64161 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21928 grid for indexing accessible points = 1.400000 m= 21266 mr = 44636 m= 2589 mr = 15614 m= 76 mr = 1515 m= 0 mr = 18 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1838 time to turn everything in is 0.5700000 number of dielectric boundary points 26309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19339 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) : 0.5844689 object centre at (A) : 37.59500 29.18400 32.17300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3121675E-02 3.2624842E-03 midg,1,midg; midg,igrid,midg -9.1853952E-03 -1.4262876E-02 1,midg,midg; igrid,midg,midg 4.2117159E-03 1.2288207E-02 gauss-seidel spectral radius is 0.9983897 estimated iterations to convergence 198 setup time was (sec) 0.9300000 now iterating at: 23:52:59 rms-change max change #iterations 3.597743 160.4546 at 10iterations 1.580110 58.71317 at 20iterations 0.6908060 26.11763 at 30iterations 0.3038073 10.46453 at 40iterations 0.1336468 5.166718 at 50iterations 5.8933035E-02 2.112608 at 60iterations 2.5972735E-02 0.8896980 at 70iterations 1.1523197E-02 0.4347367 at 80iterations 5.1800236E-03 0.1926455 at 90iterations 2.4047960E-03 9.9506378E-02 at 100iterations 1.1769920E-03 4.7771454E-02 at 110iterations 6.1380223E-04 3.0040741E-02 at 120iterations finished qdiffx linear iterations at : 23:53:07 total time elapsed so far: 9.170000 # loops : 120 mean,max change (kT/e) : 6.1380223E-04 3.0040741E-02 energy calculations done at 9.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.390000 DelPhi exited at 23:53:08 9.396u 0.286s 0:10.03 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 Mon Oct 10 2011 at 23:53:08 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2631 !!! WARNING: SEP 216 has a net charge of -0.4750 !!! WARNING: GLM 262 has a net charge of -0.0940 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: 2.630110 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): 10.40200 64.78800 ymin,ymax (A): -1.271000 59.63900 zmin,zma (A): 10.34000 54.00600 x,y,z range (A): 54.38600 60.91000 43.66600 scale (grids/A): 2.630110 object centre (A): 37.59500 29.18400 32.17300 number of atom coordinates read : 2631 total number of charged atoms : 2485 net assigned charge : 8.431020 assigned positive charge : 397.6408 centred at (gu) : 83.97585 92.67416 88.20228 assigned negative charge : -389.2104 centred at (gu) : 83.99147 92.18559 88.74300 start vw surface at 0.1800000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 148834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21928 grid for indexing accessible points = 1.400000 m= 71367 mr = 108655 m= 22905 mr = 58210 m= 4363 mr = 18305 m= 404 mr = 3206 m= 12 mr = 211 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 6362 time to turn everything in is 1.380000 number of dielectric boundary points 59293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 19874 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) : 1.753407 object centre at (A) : 37.59500 29.18400 32.17300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2910483 5.6521300E-02 midg,1,midg; midg,igrid,midg -0.3276801 -0.5263509 1,midg,midg; igrid,midg,midg 6.4358669E-03 0.1079640 gauss-seidel spectral radius is 0.9991831 estimated iterations to convergence 276 setup time was (sec) 1.750000 now iterating at: 23:53:10 rms-change max change #iterations 8.775987 267.2679 at 10iterations 4.924520 120.5144 at 20iterations 2.760987 55.78060 at 30iterations 1.549417 31.83656 at 40iterations 0.8664758 18.11299 at 50iterations 0.4830293 9.014557 at 60iterations 0.2699427 5.764549 at 70iterations 0.1507274 3.070431 at 80iterations 8.4159791E-02 1.761182 at 90iterations 4.7045678E-02 0.9519062 at 100iterations 2.6381638E-02 0.5818481 at 110iterations 1.4791426E-02 0.3207779 at 120iterations 8.3541097E-03 0.1670609 at 130iterations 4.7203456E-03 9.9374771E-02 at 140iterations 2.7224813E-03 6.7602158E-02 at 150iterations 1.6150128E-03 4.1149139E-02 at 160iterations 9.9482387E-04 2.7008057E-02 at 170iterations 6.4351043E-04 1.8936157E-02 at 180iterations finished qdiffx linear iterations at : 23:53:24 total time elapsed so far: 15.38000 # loops : 180 mean,max change (kT/e) : 6.4351043E-04 1.8936157E-02 energy calculations done at 15.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.60000 DelPhi exited at 23:53:24 15.604u 0.314s 0:16.37 97.1% 0+0k 0+0io 0pf+0w