Tue Oct 11 07:17:13 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 Tue Oct 11 2011 at 07:17:13 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3424 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: 0.5837118 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): 0.4169999 49.96400 ymin,ymax (A): -8.383000 52.60600 zmin,zma (A): 1.254000 60.70900 x,y,z range (A): 49.54700 60.98900 59.45500 scale (grids/A): 0.5837118 object centre (A): 25.19050 22.11150 30.98150 number of atom coordinates read : 3424 total number of charged atoms : 3273 net assigned charge : 6.8843365E-06 assigned positive charge : 514.7973 centred at (gu) : 89.60416 89.19353 90.51680 assigned negative charge : -514.7987 centred at (gu) : 89.50929 89.17299 90.51888 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7525 nv = 96 ne = 84 npr = 71165 no. pairs analyzed = 71165 no. exposed pairs = 4119 no. arc points = 27679 no. surface atoms = 1402 nbur = 2022 mkacc time = 0.1800000 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= 317 mr = 4232 m= 0 mr = 14 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3800000 number of dielectric boundary points 3596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2862 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9727 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9719105E-11 -4.6053366E-11 midg,1,midg; midg,igrid,midg -6.9535389E-10 5.0348103E-10 1,midg,midg; igrid,midg,midg -3.0143137E-09 2.4770970E-09 gauss-seidel spectral radius is 0.9848781 estimated iterations to convergence 67 setup time was (sec) 0.7000000 now iterating at: 07:17:14 rms-change max change #iterations 0.1096615 16.99150 at 10iterations 9.7129541E-03 1.410923 at 20iterations 1.7724485E-03 0.2757339 at 30iterations 6.6085940E-04 0.1079006 at 40iterations 2.6471855E-04 4.4055939E-02 at 50iterations finished qdiffx linear iterations at : 07:17:18 total time elapsed so far: 4.620000 # loops : 50 mean,max change (kT/e) : 2.6471855E-04 4.4055939E-02 energy calculations done at 4.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.780000 DelPhi exited at 07:17:19 4.786u 0.392s 0:05.63 91.8% 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 Tue Oct 11 2011 at 07:17:19 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3424 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: 1.751135 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): 0.4169999 49.96400 ymin,ymax (A): -8.383000 52.60600 zmin,zma (A): 1.254000 60.70900 x,y,z range (A): 49.54700 60.98900 59.45500 scale (grids/A): 1.751135 object centre (A): 25.19050 22.11150 30.98150 number of atom coordinates read : 3424 total number of charged atoms : 3273 net assigned charge : 6.8843365E-06 assigned positive charge : 514.7973 centred at (gu) : 88.81182 87.57938 91.54949 assigned negative charge : -514.7987 centred at (gu) : 88.52752 87.51829 91.55607 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27679 grid for indexing accessible points = 1.400000 m= 28260 mr = 59487 m= 3399 mr = 20588 m= 122 mr = 1937 m= 4 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 791 time to turn everything in is 0.6800000 number of dielectric boundary points 33284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 301 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 25443 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) : 0.5837118 object centre at (A) : 25.19050 22.11150 30.98150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3061536E-02 1.5483171E-03 midg,1,midg; midg,igrid,midg -1.8450754E-02 -1.8540243E-02 1,midg,midg; igrid,midg,midg -5.0999965E-03 8.9485524E-03 gauss-seidel spectral radius is 0.9984664 estimated iterations to convergence 203 setup time was (sec) 0.9700000 now iterating at: 07:17:20 rms-change max change #iterations 4.210048 191.1119 at 10iterations 1.880368 61.33125 at 20iterations 0.8448436 25.52781 at 30iterations 0.3786019 13.65747 at 40iterations 0.1706776 5.253284 at 50iterations 7.6706901E-02 2.452730 at 60iterations 3.4564294E-02 1.062950 at 70iterations 1.5700338E-02 0.5119743 at 80iterations 7.3234788E-03 0.2488079 at 90iterations 3.5948080E-03 0.1227512 at 100iterations 1.9329641E-03 7.1080208E-02 at 110iterations 1.1673246E-03 3.9539337E-02 at 120iterations finished qdiffx linear iterations at : 07:17:30 total time elapsed so far: 10.57000 # loops : 120 mean,max change (kT/e) : 1.1673246E-03 3.9539337E-02 energy calculations done at 10.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.73000 DelPhi exited at 07:17:30 10.737u 0.464s 0:11.61 96.3% 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 Tue Oct 11 2011 at 07:17:30 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3424 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: 2.626703 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): 0.4169999 49.96400 ymin,ymax (A): -8.383000 52.60600 zmin,zma (A): 1.254000 60.70900 x,y,z range (A): 49.54700 60.98900 59.45500 scale (grids/A): 2.626703 object centre (A): 25.19050 22.11150 30.98150 number of atom coordinates read : 3424 total number of charged atoms : 3273 net assigned charge : 6.8843365E-06 assigned positive charge : 514.7973 centred at (gu) : 88.21750 86.36887 92.32395 assigned negative charge : -514.7987 centred at (gu) : 87.79114 86.27750 92.33401 start vw surface at 0.1400000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 193703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27679 grid for indexing accessible points = 1.400000 m= 95383 mr = 144208 m= 29982 mr = 78033 m= 5699 mr = 23674 m= 579 mr = 4052 m= 15 mr = 312 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 2767 time to turn everything in is 1.730000 number of dielectric boundary points 75081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 26170 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) : 1.751135 object centre at (A) : 25.19050 22.11150 30.98150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2141070 -0.1341140 midg,1,midg; midg,igrid,midg -0.2671295 -0.2933917 1,midg,midg; igrid,midg,midg -6.3900255E-02 0.1134524 gauss-seidel spectral radius is 0.9992260 estimated iterations to convergence 284 setup time was (sec) 2.070000 now iterating at: 07:17:33 rms-change max change #iterations 10.26015 279.3288 at 10iterations 5.941219 134.2901 at 20iterations 3.415222 67.86346 at 30iterations 1.956708 37.82645 at 40iterations 1.118182 21.00654 at 50iterations 0.6380053 10.90304 at 60iterations 0.3644028 6.717819 at 70iterations 0.2076936 3.910358 at 80iterations 0.1184836 2.477755 at 90iterations 6.7488275E-02 1.227184 at 100iterations 3.8536239E-02 0.7373962 at 110iterations 2.1987000E-02 0.3909497 at 120iterations 1.2604358E-02 0.2165451 at 130iterations 7.3114401E-03 0.1221848 at 140iterations 4.3343361E-03 8.2237244E-02 at 150iterations 2.6560221E-03 4.7801971E-02 at 160iterations 1.7195789E-03 3.4820557E-02 at 170iterations 1.1933483E-03 2.5230408E-02 at 180iterations finished qdiffx linear iterations at : 07:17:49 total time elapsed so far: 18.51000 # loops : 180 mean,max change (kT/e) : 1.1933483E-03 2.5230408E-02 energy calculations done at 18.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.69000 DelPhi exited at 07:17:50 18.690u 0.462s 0:19.65 97.4% 0+0k 0+0io 0pf+0w