Sun Oct 9 17:32:25 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 Sun Oct 9 2011 at 17:32:26 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3208 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5719059 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): -11.08600 51.16200 ymin,ymax (A): -11.97100 40.54200 zmin,zma (A): 20.19100 75.86200 x,y,z range (A): 62.24800 52.51300 55.67100 scale (grids/A): 0.5719059 object centre (A): 20.03800 14.28550 48.02650 number of atom coordinates read : 3208 total number of charged atoms : 3061 net assigned charge : 3.621017 assigned positive charge : 495.6150 centred at (gu) : 90.93626 89.88065 87.88351 assigned negative charge : -491.9951 centred at (gu) : 90.83958 90.00116 87.83936 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7011 nv = 96 ne = 84 npr = 62805 no. pairs analyzed = 62805 no. exposed pairs = 4296 no. arc points = 30555 no. surface atoms = 1433 nbur = 1775 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 = 1.484000 m= 316 mr = 3510 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2918 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8723 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0685871E-10 8.5480673E-10 midg,1,midg; midg,igrid,midg 2.8626241E-09 -1.6163141E-09 1,midg,midg; igrid,midg,midg -9.6353647E-10 2.9462610E-09 gauss-seidel spectral radius is 0.9842449 estimated iterations to convergence 65 setup time was (sec) 0.5800000 now iterating at: 17:32:26 rms-change max change #iterations 9.6845657E-02 14.59282 at 10iterations 7.3546837E-03 1.049696 at 20iterations 5.4695143E-04 0.1034851 at 30iterations 5.1298277E-05 7.4903965E-03 at 40iterations 1.3983740E-05 1.9798279E-03 at 50iterations finished qdiffx linear iterations at : 17:32:29 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.3983740E-05 1.9798279E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 17:32:30 3.480u 0.243s 0:04.00 93.0% 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 Sun Oct 9 2011 at 17:32:30 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3208 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.715718 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): -11.08600 51.16200 ymin,ymax (A): -11.97100 40.54200 zmin,zma (A): 20.19100 75.86200 x,y,z range (A): 62.24800 52.51300 55.67100 scale (grids/A): 1.715718 object centre (A): 20.03800 14.28550 48.02650 number of atom coordinates read : 3208 total number of charged atoms : 3061 net assigned charge : 3.621017 assigned positive charge : 495.6150 centred at (gu) : 92.80779 89.64144 83.64984 assigned negative charge : -491.9951 centred at (gu) : 92.51830 90.00306 83.51768 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76247 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30555 grid for indexing accessible points = 1.400000 m= 25511 mr = 50835 m= 3196 mr = 17187 m= 125 mr = 1585 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 35461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 279 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 23692 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) : 0.5719059 object centre at (A) : 20.03800 14.28550 48.02650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4282420E-03 5.6312811E-03 midg,1,midg; midg,igrid,midg 1.9311544E-02 -1.0011785E-02 1,midg,midg; igrid,midg,midg -7.5690774E-03 1.8506920E-02 gauss-seidel spectral radius is 0.9983872 estimated iterations to convergence 198 setup time was (sec) 0.8500000 now iterating at: 17:32:31 rms-change max change #iterations 3.953081 187.5188 at 10iterations 1.735964 63.25597 at 20iterations 0.7654614 31.09728 at 30iterations 0.3364378 12.02577 at 40iterations 0.1482311 4.932394 at 50iterations 6.4933904E-02 2.270435 at 60iterations 2.8733611E-02 0.9433603 at 70iterations 1.2588694E-02 0.4277477 at 80iterations 5.5419593E-03 0.1951880 at 90iterations 2.4601815E-03 8.6437225E-02 at 100iterations 1.1107031E-03 3.7937164E-02 at 110iterations 5.3096761E-04 2.0612717E-02 at 120iterations finished qdiffx linear iterations at : 17:32:37 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 5.3096761E-04 2.0612717E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 17:32:38 7.763u 0.275s 0:08.34 96.2% 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 Sun Oct 9 2011 at 17:32:38 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3208 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.573577 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): -11.08600 51.16200 ymin,ymax (A): -11.97100 40.54200 zmin,zma (A): 20.19100 75.86200 x,y,z range (A): 62.24800 52.51300 55.67100 scale (grids/A): 2.573577 object centre (A): 20.03800 14.28550 48.02650 number of atom coordinates read : 3208 total number of charged atoms : 3061 net assigned charge : 3.621017 assigned positive charge : 495.6150 centred at (gu) : 94.21159 89.46209 80.47457 assigned negative charge : -491.9951 centred at (gu) : 93.77737 90.00458 80.27641 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 176604 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30555 grid for indexing accessible points = 1.400000 m= 84752 mr = 124550 m= 27291 mr = 66079 m= 5206 mr = 20088 m= 465 mr = 3357 m= 11 mr = 218 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 80037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 24473 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) : 1.715718 object centre at (A) : 20.03800 14.28550 48.02650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1300702 6.6146851E-02 midg,1,midg; midg,igrid,midg 0.2636277 -0.2037218 1,midg,midg; igrid,midg,midg 9.9775448E-02 0.2238532 gauss-seidel spectral radius is 0.9992126 estimated iterations to convergence 281 setup time was (sec) 1.650000 now iterating at: 17:32:40 rms-change max change #iterations 10.16365 320.3758 at 10iterations 5.976992 155.2147 at 20iterations 3.463181 85.18854 at 30iterations 1.998530 48.61964 at 40iterations 1.147266 23.64252 at 50iterations 0.6567589 13.42451 at 60iterations 0.3750482 7.953827 at 70iterations 0.2138830 4.884163 at 80iterations 0.1213004 2.480652 at 90iterations 6.9018498E-02 1.562337 at 100iterations 3.9199736E-02 0.8203964 at 110iterations 2.2248114E-02 0.4592261 at 120iterations 1.2666824E-02 0.2817464 at 130iterations 7.2026337E-03 0.1411238 at 140iterations 4.1534784E-03 8.3095551E-02 at 150iterations 2.4434358E-03 4.6964645E-02 at 160iterations 1.4986695E-03 3.5869598E-02 at 170iterations 9.8952150E-04 2.0886421E-02 at 180iterations finished qdiffx linear iterations at : 17:32:51 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 9.8952150E-04 2.0886421E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 17:32:51 12.871u 0.277s 0:13.44 97.7% 0+0k 0+0io 0pf+0w