Sat Oct 8 22:54:10 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 22:54:10 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2332 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.5913622 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): -12.46300 39.34000 ymin,ymax (A): -30.58100 29.61900 zmin,zma (A): -9.596000 32.68100 x,y,z range (A): 51.80300 60.20000 42.27700 scale (grids/A): 0.5913622 object centre (A): 13.43850 -0.4809999 11.54250 number of atom coordinates read : 2332 total number of charged atoms : 2197 net assigned charge : 10.01403 assigned positive charge : 339.6704 centred at (gu) : 89.18339 89.99085 90.98220 assigned negative charge : -329.6571 centred at (gu) : 89.17363 90.05788 90.89504 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5509 nv = 96 ne = 84 npr = 46475 no. pairs analyzed = 46475 no. exposed pairs = 3203 no. arc points = 22681 no. surface atoms = 1065 nbur = 1267 mkacc time = 9.9999994E-02 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 = 1.456000 m= 269 mr = 2712 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2323 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6893 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.2338903E-10 6.5548051E-09 midg,1,midg; midg,igrid,midg 4.7807829E-09 1.6040881E-09 1,midg,midg; igrid,midg,midg 3.5631604E-09 2.8620883E-09 gauss-seidel spectral radius is 0.9851917 estimated iterations to convergence 67 setup time was (sec) 0.5100000 now iterating at: 22:54:10 rms-change max change #iterations 9.4955258E-02 14.50995 at 10iterations 7.6341047E-03 1.293472 at 20iterations 6.1417266E-04 0.1106110 at 30iterations 5.0366292E-05 1.0026932E-02 at 40iterations 4.2793445E-06 7.0381165E-04 at 50iterations finished qdiffx linear iterations at : 22:54:13 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 4.2793445E-06 7.0381165E-04 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 22:54:13 3.162u 0.165s 0:03.60 92.2% 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 Sat Oct 8 2011 at 22:54:13 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2332 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.774086 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): -12.46300 39.34000 ymin,ymax (A): -30.58100 29.61900 zmin,zma (A): -9.596000 32.68100 x,y,z range (A): 51.80300 60.20000 42.27700 scale (grids/A): 1.774086 object centre (A): 13.43850 -0.4809999 11.54250 number of atom coordinates read : 2332 total number of charged atoms : 2197 net assigned charge : 10.01403 assigned positive charge : 339.6704 centred at (gu) : 87.54993 89.97221 92.94628 assigned negative charge : -329.6571 centred at (gu) : 87.52086 90.17346 92.68528 start vw surface at 0.1800000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 59158 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22681 grid for indexing accessible points = 1.400000 m= 19272 mr = 38392 m= 2532 mr = 13186 m= 93 mr = 1322 m= 0 mr = 9 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.4800000 number of dielectric boundary points 28146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 206 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 17161 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) : 0.5913622 object centre at (A) : 13.43850 -0.4809999 11.54250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9196946E-03 1.7648714E-02 midg,1,midg; midg,igrid,midg 3.5709683E-02 1.3775670E-02 1,midg,midg; igrid,midg,midg 2.4872337E-02 1.4392498E-02 gauss-seidel spectral radius is 0.9984152 estimated iterations to convergence 199 setup time was (sec) 0.7700000 now iterating at: 22:54:14 rms-change max change #iterations 3.424114 155.5058 at 10iterations 1.494949 62.27991 at 20iterations 0.6604557 27.26792 at 30iterations 0.2905368 10.63534 at 40iterations 0.1281988 5.023731 at 50iterations 5.6749195E-02 2.312996 at 60iterations 2.4909643E-02 0.8979044 at 70iterations 1.1026796E-02 0.4003181 at 80iterations 4.8410324E-03 0.1861515 at 90iterations 2.1395211E-03 7.2546005E-02 at 100iterations 9.4642158E-04 3.2402039E-02 at 110iterations 4.1739322E-04 1.6914368E-02 at 120iterations finished qdiffx linear iterations at : 22:54:21 total time elapsed so far: 7.200000 # loops : 120 mean,max change (kT/e) : 4.1739322E-04 1.6914368E-02 energy calculations done at 7.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.370000 DelPhi exited at 22:54:21 7.376u 0.198s 0:07.84 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 Sat Oct 8 2011 at 22:54:21 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2332 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.661130 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): -12.46300 39.34000 ymin,ymax (A): -30.58100 29.61900 zmin,zma (A): -9.596000 32.68100 x,y,z range (A): 51.80300 60.20000 42.27700 scale (grids/A): 2.661130 object centre (A): 13.43850 -0.4809999 11.54250 number of atom coordinates read : 2332 total number of charged atoms : 2197 net assigned charge : 10.01403 assigned positive charge : 339.6704 centred at (gu) : 86.32468 89.95821 94.41935 assigned negative charge : -329.6571 centred at (gu) : 86.28130 90.26020 94.02796 start vw surface at 0.1700000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 136915 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22681 grid for indexing accessible points = 1.400000 m= 63544 mr = 93975 m= 20769 mr = 49539 m= 4244 mr = 15823 m= 403 mr = 2850 m= 9 mr = 200 m= 0 mr = 0 time to grow re-entrant surface = 0.5799999 no. cavity mid-points inaccessible to solvent = 242 time to turn everything in is 1.080000 number of dielectric boundary points 63497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 17573 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) : 1.774086 object centre at (A) : 13.43850 -0.4809999 11.54250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6475189E-02 0.2010855 midg,1,midg; midg,igrid,midg 0.6271532 0.3010963 1,midg,midg; igrid,midg,midg 0.2578843 0.1591188 gauss-seidel spectral radius is 0.9992022 estimated iterations to convergence 280 setup time was (sec) 1.370000 now iterating at: 22:54:23 rms-change max change #iterations 8.419088 330.2405 at 10iterations 4.853328 133.7398 at 20iterations 2.778086 77.97468 at 30iterations 1.578913 36.37514 at 40iterations 0.8961232 20.08437 at 50iterations 0.5083326 11.19954 at 60iterations 0.2865722 6.439207 at 70iterations 0.1621327 3.595084 at 80iterations 9.1243424E-02 1.952337 at 90iterations 5.1481068E-02 1.066245 at 100iterations 2.8941162E-02 0.6146507 at 110iterations 1.6250543E-02 0.3419132 at 120iterations 9.1552027E-03 0.1811490 at 130iterations 5.1394319E-03 0.1118622 at 140iterations 2.8878765E-03 6.4338684E-02 at 150iterations 1.6253169E-03 4.1389525E-02 at 160iterations 9.1199577E-04 1.8939972E-02 at 170iterations 5.1352486E-04 1.0881424E-02 at 180iterations finished qdiffx linear iterations at : 22:54:32 total time elapsed so far: 10.70000 # loops : 180 mean,max change (kT/e) : 5.1352486E-04 1.0881424E-02 energy calculations done at 10.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.87000 DelPhi exited at 22:54:33 10.871u 0.226s 0:11.37 97.5% 0+0k 0+0io 0pf+0w