Sat Oct 8 18:11:03 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 18:11:03 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3411 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: 0.5751955 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): -1.853000 53.66100 ymin,ymax (A): -18.46100 39.04700 zmin,zma (A): -6.505000 55.38700 x,y,z range (A): 55.51400 57.50800 61.89200 scale (grids/A): 0.5751955 object centre (A): 25.90400 10.29300 24.44100 number of atom coordinates read : 3411 total number of charged atoms : 3265 net assigned charge : -5.999965 assigned positive charge : 509.0515 centred at (gu) : 89.92705 87.49718 90.91250 assigned negative charge : -515.0529 centred at (gu) : 89.97640 87.49519 90.91328 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7400 nv = 96 ne = 84 npr = 69349 no. pairs analyzed = 69349 no. exposed pairs = 4412 no. arc points = 31187 no. surface atoms = 1478 nbur = 1933 mkacc time = 0.1500000 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= 339 mr = 3869 m= 0 mr = 14 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3054 ## 329 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9515 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.7892399E-10 -1.3747713E-09 midg,1,midg; midg,igrid,midg -2.0403448E-09 -6.0138944E-10 1,midg,midg; igrid,midg,midg -4.1049157E-11 -2.1306019E-09 gauss-seidel spectral radius is 0.9844376 estimated iterations to convergence 66 setup time was (sec) 0.5700000 now iterating at: 18:11:04 rms-change max change #iterations 9.9343926E-02 15.69585 at 10iterations 7.7648074E-03 1.062543 at 20iterations 6.3197291E-04 0.1112661 at 30iterations 7.6825469E-05 1.4457226E-02 at 40iterations 1.8821847E-05 3.8833618E-03 at 50iterations finished qdiffx linear iterations at : 18:11:06 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 1.8821847E-05 3.8833618E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 18:11:07 3.202u 0.152s 0:03.63 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 18:11:07 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3411 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: 1.725587 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): -1.853000 53.66100 ymin,ymax (A): -18.46100 39.04700 zmin,zma (A): -6.505000 55.38700 x,y,z range (A): 55.51400 57.50800 61.89200 scale (grids/A): 1.725587 object centre (A): 25.90400 10.29300 24.44100 number of atom coordinates read : 3411 total number of charged atoms : 3265 net assigned charge : -5.999965 assigned positive charge : 509.0515 centred at (gu) : 89.78029 82.49042 92.73677 assigned negative charge : -515.0529 centred at (gu) : 89.92850 82.48521 92.73940 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31187 grid for indexing accessible points = 1.400000 m= 26855 mr = 55570 m= 3126 mr = 18538 m= 98 mr = 1548 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 224 time to turn everything in is 0.5700000 number of dielectric boundary points 35850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 284 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 25292 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) : 0.5751955 object centre at (A) : 25.90400 10.29300 24.44100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6021225E-03 -8.8304095E-03 midg,1,midg; midg,igrid,midg -2.6326459E-02 -1.8422640E-03 1,midg,midg; igrid,midg,midg -8.5026240E-03 -4.3778818E-02 gauss-seidel spectral radius is 0.9984252 estimated iterations to convergence 200 setup time was (sec) 0.8400000 now iterating at: 18:11:08 rms-change max change #iterations 4.037247 165.2198 at 10iterations 1.775824 60.68385 at 20iterations 0.7841809 26.72307 at 30iterations 0.3481587 12.29803 at 40iterations 0.1538388 5.364208 at 50iterations 6.8117626E-02 2.264853 at 60iterations 3.0162644E-02 1.026510 at 70iterations 1.3345638E-02 0.4224319 at 80iterations 5.9426660E-03 0.1992302 at 90iterations 2.6383048E-03 8.1533432E-02 at 100iterations 1.1800670E-03 3.6030769E-02 at 110iterations 5.2765606E-04 1.6538620E-02 at 120iterations finished qdiffx linear iterations at : 18:11:14 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 5.2765606E-04 1.6538620E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.090000 DelPhi exited at 18:11:14 7.096u 0.163s 0:07.53 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 Sat Oct 8 2011 at 18:11:14 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3411 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: 2.588380 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): -1.853000 53.66100 ymin,ymax (A): -18.46100 39.04700 zmin,zma (A): -6.505000 55.38700 x,y,z range (A): 55.51400 57.50800 61.89200 scale (grids/A): 2.588380 object centre (A): 25.90400 10.29300 24.44100 number of atom coordinates read : 3411 total number of charged atoms : 3265 net assigned charge : -5.999965 assigned positive charge : 509.0515 centred at (gu) : 89.67033 78.73545 94.10491 assigned negative charge : -515.0529 centred at (gu) : 89.89272 78.72767 94.10906 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 188858 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31187 grid for indexing accessible points = 1.400000 m= 90615 mr = 135568 m= 27711 mr = 71974 m= 4932 mr = 20745 m= 411 mr = 3213 m= 15 mr = 180 m= 0 mr = 2 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 887 time to turn everything in is 1.380000 number of dielectric boundary points 80860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 26100 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) : 1.725587 object centre at (A) : 25.90400 10.29300 24.44100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6825113E-02 3.6643758E-02 midg,1,midg; midg,igrid,midg -0.3676029 -8.9786928E-03 1,midg,midg; igrid,midg,midg -0.1466202 -0.7737808 gauss-seidel spectral radius is 0.9992230 estimated iterations to convergence 283 setup time was (sec) 1.670000 now iterating at: 18:11:16 rms-change max change #iterations 10.12835 296.1853 at 10iterations 5.885600 138.9878 at 20iterations 3.394371 66.06651 at 30iterations 1.950491 40.52497 at 40iterations 1.119284 20.86880 at 50iterations 0.6385186 11.84892 at 60iterations 0.3642615 6.909975 at 70iterations 0.2072220 4.166335 at 80iterations 0.1178229 2.336688 at 90iterations 6.7054071E-02 1.274650 at 100iterations 3.8090076E-02 0.6874958 at 110iterations 2.1606844E-02 0.4722595 at 120iterations 1.2272266E-02 0.2196293 at 130iterations 6.9558057E-03 0.1353261 at 140iterations 3.9577745E-03 7.4230194E-02 at 150iterations 2.2526935E-03 3.9908409E-02 at 160iterations 1.2846750E-03 2.4309158E-02 at 170iterations 7.3997269E-04 1.3065338E-02 at 180iterations finished qdiffx linear iterations at : 18:11:26 total time elapsed so far: 11.37000 # loops : 180 mean,max change (kT/e) : 7.3997269E-04 1.3065338E-02 energy calculations done at 11.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.55000 DelPhi exited at 18:11:26 11.553u 0.194s 0:12.07 97.2% 0+0k 0+0io 0pf+0w