Sat Oct 15 14:33:34 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 15 2011 at 14:33:34 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 = 2854 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6216168 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): -8.781000 48.48900 ymin,ymax (A): -7.949000 38.85900 zmin,zma (A): -0.1079999 55.50300 x,y,z range (A): 57.27000 46.80800 55.61100 scale (grids/A): 0.6216168 object centre (A): 19.85400 15.45500 27.69750 number of atom coordinates read : 2854 total number of charged atoms : 2713 net assigned charge : -3.499979 assigned positive charge : 427.3512 centred at (gu) : 89.22693 89.65410 88.80051 assigned negative charge : -430.8522 centred at (gu) : 89.15215 89.59284 88.81509 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7414 nv = 96 ne = 84 npr = 57664 no. pairs analyzed = 57664 no. exposed pairs = 3671 no. arc points = 26422 no. surface atoms = 1238 nbur = 1616 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 3935 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.2100000 number of dielectric boundary points 3815 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2627 ## 269 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9088 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2709088E-09 -3.1138765E-09 midg,1,midg; midg,igrid,midg -8.2628437E-09 1.6526328E-09 1,midg,midg; igrid,midg,midg -1.0342832E-08 2.3558722E-09 gauss-seidel spectral radius is 0.9866254 estimated iterations to convergence 71 setup time was (sec) 0.4600000 now iterating at: 14:33:35 rms-change max change #iterations 0.1315998 18.80654 at 10iterations 1.2304490E-02 1.687530 at 20iterations 1.1353302E-03 0.1709518 at 30iterations 1.0640454E-04 1.5599251E-02 at 40iterations 9.9446288E-06 1.2221336E-03 at 50iterations finished qdiffx linear iterations at : 14:33:40 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 9.9446288E-06 1.2221336E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 14:33:41 4.165u 0.279s 0:06.82 64.9% 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 Sat Oct 15 2011 at 14:33:41 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 = 2854 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.864851 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): -8.781000 48.48900 ymin,ymax (A): -7.949000 38.85900 zmin,zma (A): -0.1079999 55.50300 x,y,z range (A): 57.27000 46.80800 55.61100 scale (grids/A): 1.864851 object centre (A): 19.85400 15.45500 27.69750 number of atom coordinates read : 2854 total number of charged atoms : 2713 net assigned charge : -3.499979 assigned positive charge : 427.3512 centred at (gu) : 87.68021 88.96186 86.40054 assigned negative charge : -430.8522 centred at (gu) : 87.45628 88.77829 86.44463 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 80374 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26422 grid for indexing accessible points = 1.400000 m= 26918 mr = 54594 m= 3767 mr = 19126 m= 184 mr = 2164 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 837 time to turn everything in is 0.4400000 number of dielectric boundary points 35309 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 0.5400000 number of grid points assigned charge 21315 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) : 0.6216168 object centre at (A) : 19.85400 15.45500 27.69750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2621518E-02 -1.5844289E-02 midg,1,midg; midg,igrid,midg -2.2286793E-02 -8.6714001E-04 1,midg,midg; igrid,midg,midg -5.4913644E-02 2.5250003E-02 gauss-seidel spectral radius is 0.9986068 estimated iterations to convergence 212 setup time was (sec) 0.7300000 now iterating at: 14:33:43 rms-change max change #iterations 4.266196 185.0137 at 10iterations 1.980880 66.47591 at 20iterations 0.9189831 30.64754 at 30iterations 0.4255067 13.23365 at 40iterations 0.1980091 6.791367 at 50iterations 9.1877811E-02 3.064402 at 60iterations 4.2680252E-02 1.341510 at 70iterations 1.9796669E-02 0.5972633 at 80iterations 9.2091318E-03 0.2918606 at 90iterations 4.2735687E-03 0.1356525 at 100iterations 1.9898065E-03 6.1985016E-02 at 110iterations 9.2303066E-04 2.8902054E-02 at 120iterations finished qdiffx linear iterations at : 14:34:05 total time elapsed so far: 9.170000 # loops : 120 mean,max change (kT/e) : 9.2303066E-04 2.8902054E-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) 9.310000 DelPhi exited at 14:34:06 9.308u 0.306s 0:25.17 38.1% 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 15 2011 at 14:34:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2854 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.797276 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): -8.781000 48.48900 ymin,ymax (A): -7.949000 38.85900 zmin,zma (A): -0.1079999 55.50300 x,y,z range (A): 57.27000 46.80800 55.61100 scale (grids/A): 2.797276 object centre (A): 19.85400 15.45500 27.69750 number of atom coordinates read : 2854 total number of charged atoms : 2713 net assigned charge : -3.499979 assigned positive charge : 427.3512 centred at (gu) : 86.52008 88.44254 84.60061 assigned negative charge : -430.8522 centred at (gu) : 86.18444 88.16733 84.66697 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 186159 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26422 grid for indexing accessible points = 1.400000 m= 89261 mr = 132963 m= 29894 mr = 71541 m= 6387 mr = 23263 m= 795 mr = 4635 m= 27 mr = 458 m= 0 mr = 13 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 2719 time to turn everything in is 1.100000 number of dielectric boundary points 79650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 21703 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) : 1.864851 object centre at (A) : 19.85400 15.45500 27.69750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2557848 -0.4577341 midg,1,midg; midg,igrid,midg -0.2261878 -2.0348053E-02 1,midg,midg; igrid,midg,midg -0.6669867 0.3525624 gauss-seidel spectral radius is 0.9992709 estimated iterations to convergence 292 setup time was (sec) 1.460000 now iterating at: 14:34:14 rms-change max change #iterations 10.42744 349.9294 at 10iterations 6.200424 150.0300 at 20iterations 3.646230 87.46758 at 30iterations 2.137775 48.06329 at 40iterations 1.245260 24.49974 at 50iterations 0.7261821 16.00833 at 60iterations 0.4215121 7.921938 at 70iterations 0.2447861 4.808912 at 80iterations 0.1420187 2.851056 at 90iterations 8.2107499E-02 1.810635 at 100iterations 4.7468647E-02 0.8438263 at 110iterations 2.7454000E-02 0.5447063 at 120iterations 1.5866911E-02 0.2894141 at 130iterations 9.1780778E-03 0.1822705 at 140iterations 5.2994611E-03 9.3437195E-02 at 150iterations 3.0613006E-03 5.8087826E-02 at 160iterations 1.7670164E-03 3.1062603E-02 at 170iterations 1.0209902E-03 1.6827106E-02 at 180iterations finished qdiffx linear iterations at : 14:34:56 total time elapsed so far: 15.24000 # loops : 180 mean,max change (kT/e) : 1.0209902E-03 1.6827106E-02 energy calculations done at 15.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.37000 DelPhi exited at 14:34:58 15.372u 0.394s 0:50.20 31.3% 0+0k 0+0io 0pf+0w