Sat Oct 8 17:33:55 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 17:33:55 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3512 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 0.5255311 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): -0.9840000 44.98000 ymin,ymax (A): -30.57000 26.02200 zmin,zma (A): 1.607000 69.34800 x,y,z range (A): 45.96400 56.59200 67.74100 scale (grids/A): 0.5255311 object centre (A): 21.99800 -2.274000 35.47750 number of atom coordinates read : 3512 total number of charged atoms : 3365 net assigned charge : -5.871980 assigned positive charge : 539.2640 centred at (gu) : 90.35233 91.83070 90.67310 assigned negative charge : -545.1379 centred at (gu) : 90.30610 91.77818 90.66888 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6141 nv = 96 ne = 84 npr = 71564 no. pairs analyzed = 71564 no. exposed pairs = 4280 no. arc points = 29544 no. surface atoms = 1458 nbur = 2054 mkacc time = 0.1600000 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 = 1.624000 m= 219 mr = 3243 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3056 ## 477 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8245 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5111914E-10 -1.7476358E-10 midg,1,midg; midg,igrid,midg -2.2483881E-10 5.0874790E-11 1,midg,midg; igrid,midg,midg -3.0510666E-10 6.4164147E-12 gauss-seidel spectral radius is 0.9813821 estimated iterations to convergence 60 setup time was (sec) 0.5900000 now iterating at: 17:33:55 rms-change max change #iterations 6.9363810E-02 11.00665 at 10iterations 4.2936723E-03 0.7169733 at 20iterations 3.4767622E-04 8.3494186E-02 at 30iterations 6.7873130E-05 1.3977051E-02 at 40iterations 1.7947228E-05 3.6230087E-03 at 50iterations finished qdiffx linear iterations at : 17:33:58 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.7947228E-05 3.6230087E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 17:33:58 3.381u 0.164s 0:03.82 92.6% 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 17:33:59 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3512 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 1.576593 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): -0.9840000 44.98000 ymin,ymax (A): -30.57000 26.02200 zmin,zma (A): 1.607000 69.34800 x,y,z range (A): 45.96400 56.59200 67.74100 scale (grids/A): 1.576593 object centre (A): 21.99800 -2.274000 35.47750 number of atom coordinates read : 3512 total number of charged atoms : 3365 net assigned charge : -5.871980 assigned positive charge : 539.2640 centred at (gu) : 91.05608 95.49095 92.01840 assigned negative charge : -545.1379 centred at (gu) : 90.91778 95.33442 92.00638 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69250 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29544 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20821 mr = 48059 m= 1835 mr = 14098 m= 37 mr = 784 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 258 time to turn everything in is 0.5100000 number of dielectric boundary points 29002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 421 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 25515 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) : 0.5255311 object centre at (A) : 21.99800 -2.274000 35.47750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6726167E-03 8.6239623E-03 midg,1,midg; midg,igrid,midg -8.9589069E-03 -1.2341242E-02 1,midg,midg; igrid,midg,midg -4.8927357E-03 1.7588582E-03 gauss-seidel spectral radius is 0.9980886 estimated iterations to convergence 182 setup time was (sec) 0.7900000 now iterating at: 17:33:59 rms-change max change #iterations 3.444981 164.1207 at 10iterations 1.396479 55.96601 at 20iterations 0.5699946 19.64785 at 30iterations 0.2332021 7.968212 at 40iterations 9.5133461E-02 3.390594 at 50iterations 3.8850520E-02 1.297986 at 60iterations 1.5862396E-02 0.5931463 at 70iterations 6.5256115E-03 0.2411957 at 80iterations 2.6754746E-03 8.6913466E-02 at 90iterations 1.1174247E-03 4.0673256E-02 at 100iterations 4.7854264E-04 1.7939091E-02 at 110iterations 2.1478727E-04 8.2550049E-03 at 120iterations finished qdiffx linear iterations at : 17:34:06 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 2.1478727E-04 8.2550049E-03 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.420000 DelPhi exited at 17:34:06 7.421u 0.193s 0:07.95 95.7% 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 Sat Oct 8 2011 at 17:34:07 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3512 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 2.364890 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): -0.9840000 44.98000 ymin,ymax (A): -30.57000 26.02200 zmin,zma (A): 1.607000 69.34800 x,y,z range (A): 45.96400 56.59200 67.74100 scale (grids/A): 2.364890 object centre (A): 21.99800 -2.274000 35.47750 number of atom coordinates read : 3512 total number of charged atoms : 3365 net assigned charge : -5.871980 assigned positive charge : 539.2640 centred at (gu) : 91.58385 98.23622 93.02739 assigned negative charge : -545.1379 centred at (gu) : 91.37656 98.00159 93.00954 start vw surface at 0.1800000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 161143 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29544 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 74022 mr = 117790 m= 19282 mr = 58300 m= 2633 mr = 14025 m= 122 mr = 1590 m= 0 mr = 41 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 680 time to turn everything in is 1.200000 number of dielectric boundary points 65456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 26845 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) : 1.576593 object centre at (A) : 21.99800 -2.274000 35.47750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2260641 1.9445673E-02 midg,1,midg; midg,igrid,midg -0.1265554 -0.1492821 1,midg,midg; igrid,midg,midg -8.2501397E-02 4.5444351E-02 gauss-seidel spectral radius is 0.9991151 estimated iterations to convergence 266 setup time was (sec) 1.520000 now iterating at: 17:34:08 rms-change max change #iterations 9.167064 322.7400 at 10iterations 5.108562 113.4472 at 20iterations 2.840510 71.95148 at 30iterations 1.563773 35.55193 at 40iterations 0.8607043 18.64491 at 50iterations 0.4722830 10.44125 at 60iterations 0.2590170 5.274480 at 70iterations 0.1414070 2.992313 at 80iterations 7.7336833E-02 1.620012 at 90iterations 4.2265214E-02 0.8879776 at 100iterations 2.3126734E-02 0.4892235 at 110iterations 1.2585395E-02 0.2659874 at 120iterations 6.8827900E-03 0.1375027 at 130iterations 3.7670387E-03 8.1443787E-02 at 140iterations 2.0587028E-03 4.0469170E-02 at 150iterations 1.1292173E-03 2.4341583E-02 at 160iterations 6.2364119E-04 1.3193130E-02 at 170iterations 3.4731909E-04 6.8588257E-03 at 180iterations finished qdiffx linear iterations at : 17:34:19 total time elapsed so far: 11.86000 # loops : 180 mean,max change (kT/e) : 3.4731909E-04 6.8588257E-03 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.05000 DelPhi exited at 17:34:19 12.052u 0.201s 0:12.52 97.8% 0+0k 0+0io 0pf+0w