Sat Oct 8 15:20:39 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 8 2011 at 15:20:39 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3217 !!! WARNING: SEP 64 has a net charge of -0.4750 !!! WARNING: GLM 120 has a net charge of -0.0940 !!! WARNING: SEP 318 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5793988 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): -6.003000 49.54100 ymin,ymax (A): -12.99800 38.49000 zmin,zma (A): -7.945000 53.49800 x,y,z range (A): 55.54400 51.48800 61.44300 scale (grids/A): 0.5793988 object centre (A): 21.76900 12.74600 22.77650 number of atom coordinates read : 3217 total number of charged atoms : 3065 net assigned charge : 1.456011 assigned positive charge : 478.8149 centred at (gu) : 88.65874 89.39448 89.47289 assigned negative charge : -477.3600 centred at (gu) : 88.61126 89.37598 89.50719 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7015 nv = 96 ne = 84 npr = 66175 no. pairs analyzed = 66175 no. exposed pairs = 3700 no. arc points = 25639 no. surface atoms = 1256 nbur = 1961 mkacc time = 0.1400000 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 = 1.512000 m= 311 mr = 3926 m= 0 mr = 23 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3300000 number of dielectric boundary points 3377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2612 ## 285 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8985 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2636779E-09 -4.1341799E-10 midg,1,midg; midg,igrid,midg -1.2124532E-10 6.5348149E-10 1,midg,midg; igrid,midg,midg -1.0816686E-09 1.0354250E-09 gauss-seidel spectral radius is 0.9846399 estimated iterations to convergence 66 setup time was (sec) 0.5500000 now iterating at: 15:20:39 rms-change max change #iterations 0.1027921 16.22016 at 10iterations 8.2087405E-03 1.229481 at 20iterations 6.7323167E-04 0.1246858 at 30iterations 5.9189577E-05 8.8138580E-03 at 40iterations 6.8682675E-06 9.8800659E-04 at 50iterations finished qdiffx linear iterations at : 15:20:42 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 6.8682675E-06 9.8800659E-04 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 15:20:42 3.133u 0.140s 0:03.55 92.1% 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 15:20:42 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3217 !!! WARNING: SEP 64 has a net charge of -0.4750 !!! WARNING: GLM 120 has a net charge of -0.0940 !!! WARNING: SEP 318 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.738196 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): -6.003000 49.54100 ymin,ymax (A): -12.99800 38.49000 zmin,zma (A): -7.945000 53.49800 x,y,z range (A): 55.54400 51.48800 61.44300 scale (grids/A): 1.738196 object centre (A): 21.76900 12.74600 22.77650 number of atom coordinates read : 3217 total number of charged atoms : 3065 net assigned charge : 1.456011 assigned positive charge : 478.8149 centred at (gu) : 85.97533 88.18258 88.41803 assigned negative charge : -477.3600 centred at (gu) : 85.83342 88.12758 88.52112 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25639 grid for indexing accessible points = 1.400000 m= 26431 mr = 55212 m= 3422 mr = 19290 m= 118 mr = 1949 m= 0 mr = 19 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2133 time to turn everything in is 0.5300000 number of dielectric boundary points 31306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 249 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 23851 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) : 0.5793988 object centre at (A) : 21.76900 12.74600 22.77650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0380164E-02 7.3579340E-03 midg,1,midg; midg,igrid,midg 4.7323876E-03 4.6841861E-03 1,midg,midg; igrid,midg,midg -4.3488280E-03 4.6896953E-03 gauss-seidel spectral radius is 0.9984233 estimated iterations to convergence 200 setup time was (sec) 0.8000000 now iterating at: 15:20:43 rms-change max change #iterations 3.932251 169.5107 at 10iterations 1.738634 57.20195 at 20iterations 0.7694402 23.73738 at 30iterations 0.3402106 11.48462 at 40iterations 0.1512002 4.395466 at 50iterations 6.6955924E-02 2.197250 at 60iterations 2.9668473E-02 0.9163322 at 70iterations 1.3135171E-02 0.4347112 at 80iterations 5.8273454E-03 0.1800175 at 90iterations 2.5863277E-03 9.4863892E-02 at 100iterations 1.1501861E-03 3.7158966E-02 at 110iterations 5.0951855E-04 1.6517639E-02 at 120iterations finished qdiffx linear iterations at : 15:20:49 total time elapsed so far: 6.720000 # loops : 120 mean,max change (kT/e) : 5.0951855E-04 1.6517639E-02 energy calculations done at 6.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 15:20:50 6.893u 0.177s 0:07.34 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 15:20:50 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3217 !!! WARNING: SEP 64 has a net charge of -0.4750 !!! WARNING: GLM 120 has a net charge of -0.0940 !!! WARNING: SEP 318 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.607295 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): -6.003000 49.54100 ymin,ymax (A): -12.99800 38.49000 zmin,zma (A): -7.945000 53.49800 x,y,z range (A): 55.54400 51.48800 61.44300 scale (grids/A): 2.607295 object centre (A): 21.76900 12.74600 22.77650 number of atom coordinates read : 3217 total number of charged atoms : 3065 net assigned charge : 1.456011 assigned positive charge : 478.8149 centred at (gu) : 83.96259 87.27372 87.62677 assigned negative charge : -477.3600 centred at (gu) : 83.75001 87.19122 87.78154 start vw surface at 0.1700000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 180348 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25639 grid for indexing accessible points = 1.400000 m= 88992 mr = 133918 m= 28772 mr = 72665 m= 5845 mr = 22714 m= 612 mr = 4236 m= 16 mr = 368 m= 0 mr = 0 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 7229 time to turn everything in is 1.300000 number of dielectric boundary points 70684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 24509 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) : 1.738196 object centre at (A) : 21.76900 12.74600 22.77650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2565963 5.5237032E-02 midg,1,midg; midg,igrid,midg 6.5320842E-02 3.2666195E-02 1,midg,midg; igrid,midg,midg 5.5522997E-02 4.8615865E-02 gauss-seidel spectral radius is 0.9992101 estimated iterations to convergence 281 setup time was (sec) 1.570000 now iterating at: 15:20:51 rms-change max change #iterations 9.676871 288.2256 at 10iterations 5.555018 142.1154 at 20iterations 3.169255 73.30390 at 30iterations 1.806126 33.96059 at 40iterations 1.023959 19.23990 at 50iterations 0.5809116 12.11253 at 60iterations 0.3285531 6.588678 at 70iterations 0.1860231 3.645767 at 80iterations 0.1049576 1.876584 at 90iterations 5.9354343E-02 1.165250 at 100iterations 3.3526119E-02 0.6080685 at 110iterations 1.8903084E-02 0.3371944 at 120iterations 1.0667749E-02 0.1912403 at 130iterations 6.0226931E-03 0.1097255 at 140iterations 3.3975106E-03 6.3583374E-02 at 150iterations 1.9148312E-03 3.4069061E-02 at 160iterations 1.0826500E-03 1.9880295E-02 at 170iterations 6.1090535E-04 1.0700226E-02 at 180iterations finished qdiffx linear iterations at : 15:21:01 total time elapsed so far: 11.03000 # loops : 180 mean,max change (kT/e) : 6.1090535E-04 1.0700226E-02 energy calculations done at 11.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.19000 DelPhi exited at 15:21:01 11.192u 0.185s 0:11.65 97.5% 0+0k 0+0io 0pf+0w