Sun Oct 9 20:59:16 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 Sun Oct 9 2011 at 20:59:16 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3238 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: CYS 258 has a net charge of 0.5000 !!! WARNING: GLM 421 has a net charge of -0.6000 !!! WARNING: GLM 555 has a net charge of -0.6000 !!! WARNING: HIZ 559 has a net charge of 0.2000 !!! WARNING: ZN7 775 has a net charge of 1.4000 !!! WARNING: ZN7 779 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6353171 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): 45.30000 98.37800 ymin,ymax (A): 2.976000 59.01100 zmin,zma (A): 15.06100 67.42900 x,y,z range (A): 53.07800 56.03500 52.36800 scale (grids/A): 0.6353171 object centre (A): 71.83900 30.99350 41.24500 number of atom coordinates read : 3238 total number of charged atoms : 3088 net assigned charge : 7.400014 assigned positive charge : 492.9076 centred at (gu) : 90.40244 88.02551 90.51572 assigned negative charge : -485.5091 centred at (gu) : 90.31522 87.97305 90.54855 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8932 nv = 96 ne = 84 npr = 63439 no. pairs analyzed = 63439 no. exposed pairs = 4225 no. arc points = 30694 no. surface atoms = 1408 nbur = 1830 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 442 mr = 4707 m= 3 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 41 time to turn everything in is 0.3200000 number of dielectric boundary points 4628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3031 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 10720 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2263085E-08 5.8591176E-09 midg,1,midg; midg,igrid,midg 3.9316403E-09 1.0665842E-08 1,midg,midg; igrid,midg,midg -1.5625089E-09 2.2381263E-08 gauss-seidel spectral radius is 0.9872317 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 20:59:17 rms-change max change #iterations 0.1599174 31.00920 at 10iterations 1.5349906E-02 2.698769 at 20iterations 1.5085591E-03 0.2247391 at 30iterations 1.4865803E-04 2.0526886E-02 at 40iterations 1.5135640E-05 2.1324158E-03 at 50iterations finished qdiffx linear iterations at : 20:59:19 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 1.5135640E-05 2.1324158E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 20:59:20 3.095u 0.157s 0:03.53 91.7% 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 20:59:20 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3238 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: CYS 258 has a net charge of 0.5000 !!! WARNING: GLM 421 has a net charge of -0.6000 !!! WARNING: GLM 555 has a net charge of -0.6000 !!! WARNING: HIZ 559 has a net charge of 0.2000 !!! WARNING: ZN7 775 has a net charge of 1.4000 !!! WARNING: ZN7 779 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.905951 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): 45.30000 98.37800 ymin,ymax (A): 2.976000 59.01100 zmin,zma (A): 15.06100 67.42900 x,y,z range (A): 53.07800 56.03500 52.36800 scale (grids/A): 1.905951 object centre (A): 71.83900 30.99350 41.24500 number of atom coordinates read : 3238 total number of charged atoms : 3088 net assigned charge : 7.400014 assigned positive charge : 492.9076 centred at (gu) : 91.20670 84.07568 91.54602 assigned negative charge : -485.5091 centred at (gu) : 90.94521 83.91874 91.64534 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 95719 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30694 grid for indexing accessible points = 1.400000 m= 33119 mr = 64796 m= 5147 mr = 23486 m= 322 mr = 2941 m= 4 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 3177 time to turn everything in is 0.6300000 number of dielectric boundary points 42991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 24255 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) : 0.6353171 object centre at (A) : 71.83900 30.99350 41.24500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6174217E-03 -1.4781399E-02 midg,1,midg; midg,igrid,midg 0.1005643 3.8937483E-02 1,midg,midg; igrid,midg,midg -2.1054907E-02 2.7046340E-02 gauss-seidel spectral radius is 0.9987125 estimated iterations to convergence 221 setup time was (sec) 0.8800000 now iterating at: 20:59:21 rms-change max change #iterations 4.843126 184.7416 at 10iterations 2.308683 66.64462 at 20iterations 1.103791 34.04343 at 30iterations 0.5257969 16.59391 at 40iterations 0.2508647 7.361080 at 50iterations 0.1203051 3.782648 at 60iterations 5.7537403E-02 1.735591 at 70iterations 2.7549492E-02 0.7590742 at 80iterations 1.3130018E-02 0.3856426 at 90iterations 6.2878584E-03 0.1919127 at 100iterations 3.0033339E-03 9.4238281E-02 at 110iterations 1.4404018E-03 3.9838791E-02 at 120iterations finished qdiffx linear iterations at : 20:59:27 total time elapsed so far: 6.940000 # loops : 120 mean,max change (kT/e) : 1.4404018E-03 3.9838791E-02 energy calculations done at 6.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.110000 DelPhi exited at 20:59:27 7.116u 0.176s 0:07.57 96.1% 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 Sun Oct 9 2011 at 20:59:27 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3238 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: CYS 258 has a net charge of 0.5000 !!! WARNING: GLM 421 has a net charge of -0.6000 !!! WARNING: GLM 555 has a net charge of -0.6000 !!! WARNING: HIZ 559 has a net charge of 0.2000 !!! WARNING: ZN7 775 has a net charge of 1.4000 !!! WARNING: ZN7 779 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: 2.858927 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): 45.30000 98.37800 ymin,ymax (A): 2.976000 59.01100 zmin,zma (A): 15.06100 67.42900 x,y,z range (A): 53.07800 56.03500 52.36800 scale (grids/A): 2.858927 object centre (A): 71.83900 30.99350 41.24500 number of atom coordinates read : 3238 total number of charged atoms : 3088 net assigned charge : 7.400014 assigned positive charge : 492.9076 centred at (gu) : 91.80973 81.11327 92.31884 assigned negative charge : -485.5091 centred at (gu) : 91.41776 80.87804 92.46805 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 221430 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30694 grid for indexing accessible points = 1.400000 m= 108092 mr = 157310 m= 37475 mr = 86692 m= 8952 mr = 29066 m= 1353 mr = 6303 m= 93 mr = 860 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 10756 time to turn everything in is 1.570000 number of dielectric boundary points 97117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 24700 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) : 1.905951 object centre at (A) : 71.83900 30.99350 41.24500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1280267 -0.3124398 midg,1,midg; midg,igrid,midg 0.8817556 0.4014978 1,midg,midg; igrid,midg,midg -0.2666359 0.3130073 gauss-seidel spectral radius is 0.9993027 estimated iterations to convergence 299 setup time was (sec) 1.850000 now iterating at: 20:59:29 rms-change max change #iterations 11.54669 326.7615 at 10iterations 6.968966 176.1661 at 20iterations 4.183252 104.9283 at 30iterations 2.496744 47.72039 at 40iterations 1.481398 29.78807 at 50iterations 0.8751388 16.08581 at 60iterations 0.5180799 9.273386 at 70iterations 0.3049948 5.503907 at 80iterations 0.1791412 3.302831 at 90iterations 0.1053807 2.059423 at 100iterations 6.1963834E-02 1.008749 at 110iterations 3.6318395E-02 0.5831771 at 120iterations 2.1341678E-02 0.3598976 at 130iterations 1.2492939E-02 0.2180347 at 140iterations 7.3248604E-03 0.1334133 at 150iterations 4.2876313E-03 6.9808960E-02 at 160iterations 2.5140240E-03 3.9142609E-02 at 170iterations 1.4733578E-03 2.5487900E-02 at 180iterations finished qdiffx linear iterations at : 20:59:39 total time elapsed so far: 11.53000 # loops : 180 mean,max change (kT/e) : 1.4733578E-03 2.5487900E-02 energy calculations done at 11.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 20:59:40 11.704u 0.182s 0:12.16 97.6% 0+0k 0+0io 0pf+0w