Tue Oct 11 05:17:14 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 Tue Oct 11 2011 at 05:17:14 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2320 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG6 682 has a net charge of 1.4000 !!! WARNING: ZN6 683 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: 0.6900562 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): 15.69300 62.99700 ymin,ymax (A): -3.522000 33.68800 zmin,zma (A): 20.11800 71.70800 x,y,z range (A): 47.30400 37.21000 51.59000 scale (grids/A): 0.6900562 object centre (A): 39.34500 15.08300 45.91300 number of atom coordinates read : 2320 total number of charged atoms : 1996 net assigned charge : 9.000009 assigned positive charge : 327.3739 centred at (gu) : 91.42052 89.65746 89.18032 assigned negative charge : -318.3741 centred at (gu) : 91.52393 89.66309 89.10529 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6807 nv = 96 ne = 84 npr = 42732 no. pairs analyzed = 42732 no. exposed pairs = 2598 no. arc points = 17701 no. surface atoms = 882 nbur = 1438 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 3916 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1712 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7711 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8965069E-08 6.4494088E-08 midg,1,midg; midg,igrid,midg 5.6016717E-08 4.5531909E-08 1,midg,midg; igrid,midg,midg 6.4475728E-08 1.9227357E-08 gauss-seidel spectral radius is 0.9890611 estimated iterations to convergence 78 setup time was (sec) 0.6500000 now iterating at: 05:17:15 rms-change max change #iterations 0.1891218 27.60269 at 10iterations 2.1910705E-02 2.927988 at 20iterations 2.5913543E-03 0.3600799 at 30iterations 3.0593676E-04 4.1770935E-02 at 40iterations 3.6400666E-05 4.8666000E-03 at 50iterations finished qdiffx linear iterations at : 05:17:18 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 3.6400666E-05 4.8666000E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.220000 DelPhi exited at 05:17:19 4.226u 0.204s 0:05.09 86.8% 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 Tue Oct 11 2011 at 05:17:19 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2320 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG6 682 has a net charge of 1.4000 !!! WARNING: ZN6 683 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: 2.070169 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): 15.69300 62.99700 ymin,ymax (A): -3.522000 33.68800 zmin,zma (A): 20.11800 71.70800 x,y,z range (A): 47.30400 37.21000 51.59000 scale (grids/A): 2.070169 object centre (A): 39.34500 15.08300 45.91300 number of atom coordinates read : 2320 total number of charged atoms : 1996 net assigned charge : 9.000009 assigned positive charge : 327.3739 centred at (gu) : 94.26148 88.97224 87.54108 assigned negative charge : -318.3741 centred at (gu) : 94.57197 88.98937 87.31586 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72142 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17701 grid for indexing accessible points = 1.400000 m= 28797 mr = 50987 m= 5640 mr = 21921 m= 486 mr = 3762 m= 10 mr = 239 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 146 time to turn everything in is 0.7000000 number of dielectric boundary points 30166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 82 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 15840 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) : 0.6900562 object centre at (A) : 39.34500 15.08300 45.91300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7821756E-02 4.7607046E-02 midg,1,midg; midg,igrid,midg 2.8281691E-02 2.4436772E-02 1,midg,midg; igrid,midg,midg 2.7120052E-02 3.0357707E-02 gauss-seidel spectral radius is 0.9987816 estimated iterations to convergence 227 setup time was (sec) 1.070000 now iterating at: 05:17:20 rms-change max change #iterations 4.481539 238.2841 at 10iterations 2.199319 73.00649 at 20iterations 1.064605 39.72425 at 30iterations 0.5243097 15.50618 at 40iterations 0.2553543 8.053009 at 50iterations 0.1249534 3.703784 at 60iterations 6.1109398E-02 2.097805 at 70iterations 2.9805910E-02 0.8580189 at 80iterations 1.4600330E-02 0.4869347 at 90iterations 7.1258848E-03 0.2427902 at 100iterations 3.4830922E-03 0.1148338 at 110iterations 1.7030962E-03 5.4311752E-02 at 120iterations finished qdiffx linear iterations at : 05:17:28 total time elapsed so far: 9.240000 # loops : 120 mean,max change (kT/e) : 1.7030962E-03 5.4311752E-02 energy calculations done at 9.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.460000 DelPhi exited at 05:17:29 9.467u 0.245s 0:10.30 94.1% 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 Tue Oct 11 2011 at 05:17:29 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2320 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG6 682 has a net charge of 1.4000 !!! WARNING: ZN6 683 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: 3.105253 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): 15.69300 62.99700 ymin,ymax (A): -3.522000 33.68800 zmin,zma (A): 20.11800 71.70800 x,y,z range (A): 47.30400 37.21000 51.59000 scale (grids/A): 3.105253 object centre (A): 39.34500 15.08300 45.91300 number of atom coordinates read : 2320 total number of charged atoms : 1996 net assigned charge : 9.000009 assigned positive charge : 327.3739 centred at (gu) : 96.39218 88.45833 86.31152 assigned negative charge : -318.3741 centred at (gu) : 96.85793 88.48405 85.97382 start vw surface at 0.1600000 fill in re-entrant regions at 0.9900000 boundary points on vw surface= 166140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17701 grid for indexing accessible points = 1.400000 m= 90058 mr = 122585 m= 36179 mr = 75036 m= 10478 mr = 29755 m= 2042 mr = 8192 m= 206 mr = 1515 m= 4 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 452 time to turn everything in is 2.220000 number of dielectric boundary points 67908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.380000 number of grid points assigned charge 15968 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) : 2.070169 object centre at (A) : 39.34500 15.08300 45.91300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4392728 0.3589796 midg,1,midg; midg,igrid,midg 0.2510990 0.2186313 1,midg,midg; igrid,midg,midg 0.2231929 0.5323118 gauss-seidel spectral radius is 0.9992864 estimated iterations to convergence 295 setup time was (sec) 2.600000 now iterating at: 05:17:32 rms-change max change #iterations 10.15314 378.1315 at 10iterations 5.975011 141.8063 at 20iterations 3.517697 81.88230 at 30iterations 2.066202 46.03500 at 40iterations 1.208700 26.37242 at 50iterations 0.7084363 14.96005 at 60iterations 0.4131457 7.614979 at 70iterations 0.2412248 5.139874 at 80iterations 0.1409489 2.622906 at 90iterations 8.2272798E-02 1.638859 at 100iterations 4.7987219E-02 0.8368683 at 110iterations 2.7944425E-02 0.5003471 at 120iterations 1.6258359E-02 0.2970872 at 130iterations 9.5173521E-03 0.1703339 at 140iterations 5.5595352E-03 0.1000824 at 150iterations 3.2587685E-03 5.9005737E-02 at 160iterations 1.9210459E-03 3.9436340E-02 at 170iterations 1.1501358E-03 2.1877527E-02 at 180iterations finished qdiffx linear iterations at : 05:17:46 total time elapsed so far: 16.21000 # loops : 180 mean,max change (kT/e) : 1.1501358E-03 2.1877527E-02 energy calculations done at 16.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.44000 DelPhi exited at 05:17:46 16.442u 0.263s 0:17.11 97.6% 0+0k 0+0io 0pf+0w