Sat Oct 8 19:49:43 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 19:49:43 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2436 !!! WARNING: HIR 64 has a net charge of 0.5140 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 461 has a net charge of 1.4000 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: 0.6604334 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): -30.77300 17.06100 ymin,ymax (A): -23.51600 23.19000 zmin,zma (A): -12.10500 41.79900 x,y,z range (A): 47.83400 46.70600 53.90400 scale (grids/A): 0.6604334 object centre (A): -6.856000 -0.1629992 14.84700 number of atom coordinates read : 2436 total number of charged atoms : 2292 net assigned charge : 4.420006 assigned positive charge : 366.6203 centred at (gu) : 88.73563 89.26434 89.72693 assigned negative charge : -362.2008 centred at (gu) : 88.61322 89.35842 89.57854 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6878 nv = 96 ne = 84 npr = 51973 no. pairs analyzed = 51973 no. exposed pairs = 2720 no. arc points = 19196 no. surface atoms = 917 nbur = 1519 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 3990 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 192 time to turn everything in is 0.3600000 number of dielectric boundary points 3194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1777 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8191 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7449848E-08 3.6719914E-08 midg,1,midg; midg,igrid,midg 3.3817663E-08 -5.0891305E-09 1,midg,midg; igrid,midg,midg -1.5232294E-08 2.6310028E-08 gauss-seidel spectral radius is 0.9880937 estimated iterations to convergence 75 setup time was (sec) 0.6800000 now iterating at: 19:49:44 rms-change max change #iterations 0.1630643 21.62178 at 10iterations 1.7406035E-02 2.329574 at 20iterations 1.8530196E-03 0.3233833 at 30iterations 1.9680134E-04 2.6919365E-02 at 40iterations 2.1825037E-05 2.8266907E-03 at 50iterations finished qdiffx linear iterations at : 19:49:48 total time elapsed so far: 4.180000 # loops : 50 mean,max change (kT/e) : 2.1825037E-05 2.8266907E-03 energy calculations done at 4.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 19:49:48 4.402u 0.414s 0:05.09 94.4% 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 19:49:48 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2436 !!! WARNING: HIR 64 has a net charge of 0.5140 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 461 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.981300 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): -30.77300 17.06100 ymin,ymax (A): -23.51600 23.19000 zmin,zma (A): -12.10500 41.79900 x,y,z range (A): 47.83400 46.70600 53.90400 scale (grids/A): 1.981300 object centre (A): -6.856000 -0.1629992 14.84700 number of atom coordinates read : 2436 total number of charged atoms : 2292 net assigned charge : 4.420006 assigned positive charge : 366.6203 centred at (gu) : 86.20656 87.79240 89.18052 assigned negative charge : -362.2008 centred at (gu) : 85.83953 88.07507 88.73562 start vw surface at 0.1400000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 74194 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19196 grid for indexing accessible points = 1.400000 m= 26887 mr = 52869 m= 4546 mr = 20373 m= 286 mr = 3100 m= 5 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 5098 time to turn everything in is 0.7500000 number of dielectric boundary points 29451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 18100 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) : 0.6604334 object centre at (A) : -6.856000 -0.1629992 14.84700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4177486E-02 3.4196291E-02 midg,1,midg; midg,igrid,midg 2.8773809E-02 -2.6514209E-03 1,midg,midg; igrid,midg,midg -4.9291411E-03 4.7421429E-02 gauss-seidel spectral radius is 0.9987083 estimated iterations to convergence 220 setup time was (sec) 1.080000 now iterating at: 19:49:50 rms-change max change #iterations 4.414137 182.8441 at 10iterations 2.113573 69.79565 at 20iterations 1.011449 30.39098 at 30iterations 0.4844855 15.50182 at 40iterations 0.2324116 7.202110 at 50iterations 0.1114104 3.454041 at 60iterations 5.3254087E-02 1.561247 at 70iterations 2.5571546E-02 0.8850422 at 80iterations 1.2199393E-02 0.3865471 at 90iterations 5.8478997E-03 0.1881695 at 100iterations 2.7991200E-03 9.3692780E-02 at 110iterations 1.3408407E-03 3.9551735E-02 at 120iterations finished qdiffx linear iterations at : 19:49:59 total time elapsed so far: 10.12000 # loops : 120 mean,max change (kT/e) : 1.3408407E-03 3.9551735E-02 energy calculations done at 10.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.33000 DelPhi exited at 19:50:00 10.338u 0.463s 0:11.10 97.2% 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 19:50:00 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2436 !!! WARNING: HIR 64 has a net charge of 0.5140 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 461 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.971950 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): -30.77300 17.06100 ymin,ymax (A): -23.51600 23.19000 zmin,zma (A): -12.10500 41.79900 x,y,z range (A): 47.83400 46.70600 53.90400 scale (grids/A): 2.971950 object centre (A): -6.856000 -0.1629992 14.84700 number of atom coordinates read : 2436 total number of charged atoms : 2292 net assigned charge : 4.420006 assigned positive charge : 366.6203 centred at (gu) : 84.30980 86.68857 88.77071 assigned negative charge : -362.2008 centred at (gu) : 83.75935 87.11266 88.10336 start vw surface at 0.1600000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 171919 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19196 grid for indexing accessible points = 1.400000 m= 87106 mr = 127895 m= 32141 mr = 72494 m= 8527 mr = 26543 m= 1281 mr = 6750 m= 80 mr = 900 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 17155 time to turn everything in is 2.030000 number of dielectric boundary points 66436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 18336 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) : 1.981300 object centre at (A) : -6.856000 -0.1629992 14.84700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1091834 0.3434153 midg,1,midg; midg,igrid,midg 0.2755792 -6.3788921E-02 1,midg,midg; igrid,midg,midg 1.0539723E-02 0.5135236 gauss-seidel spectral radius is 0.9992650 estimated iterations to convergence 291 setup time was (sec) 2.400000 now iterating at: 19:50:02 rms-change max change #iterations 10.05172 480.6868 at 10iterations 5.824434 115.7668 at 20iterations 3.367459 71.38245 at 30iterations 1.944946 33.56491 at 40iterations 1.126630 21.69003 at 50iterations 0.6484056 11.30370 at 60iterations 0.3750431 6.441967 at 70iterations 0.2158341 3.889643 at 80iterations 0.1244530 2.263561 at 90iterations 7.1612962E-02 1.443317 at 100iterations 4.1393463E-02 0.8461456 at 110iterations 2.3843847E-02 0.4641962 at 120iterations 1.3725964E-02 0.2682095 at 130iterations 7.9281107E-03 0.1414690 at 140iterations 4.5774258E-03 8.8603973E-02 at 150iterations 2.6512784E-03 5.0468445E-02 at 160iterations 1.5356460E-03 2.6523590E-02 at 170iterations 8.9165964E-04 1.5535355E-02 at 180iterations finished qdiffx linear iterations at : 19:50:21 total time elapsed so far: 21.25000 # loops : 180 mean,max change (kT/e) : 8.9165964E-04 1.5535355E-02 energy calculations done at 21.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.47000 DelPhi exited at 19:50:22 21.472u 0.461s 0:22.24 98.6% 0+0k 0+0io 0pf+0w