Sat Oct 15 15:14:24 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 15 2011 at 15:14:24 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: 388 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: SEP 250 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6085470 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): -7.791000 50.70900 ymin,ymax (A): 7.296999 61.76500 zmin,zma (A): 1.057000 55.92100 x,y,z range (A): 58.50000 54.46800 54.86400 scale (grids/A): 0.6085470 object centre (A): 21.45900 34.53100 28.48900 number of atom coordinates read : 2809 total number of charged atoms : 2599 net assigned charge : 6.039018 assigned positive charge : 418.8239 centred at (gu) : 90.27411 90.95099 90.93670 assigned negative charge : -412.7853 centred at (gu) : 90.55640 90.82504 90.76495 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6675 nv = 96 ne = 84 npr = 57989 no. pairs analyzed = 57989 no. exposed pairs = 3415 no. arc points = 23883 no. surface atoms = 1170 nbur = 1639 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 369 mr = 3541 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2281 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8170 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4123998E-09 1.4579562E-08 midg,1,midg; midg,igrid,midg -2.4763456E-09 1.1855368E-08 1,midg,midg; igrid,midg,midg 1.6056392E-08 -1.2106375E-08 gauss-seidel spectral radius is 0.9860343 estimated iterations to convergence 69 setup time was (sec) 0.6800000 now iterating at: 15:14:25 rms-change max change #iterations 0.1242769 17.24367 at 10iterations 1.1029304E-02 1.565100 at 20iterations 1.0531101E-03 0.1443176 at 30iterations 1.6547198E-04 2.2430420E-02 at 40iterations 5.3920361E-05 6.0443878E-03 at 50iterations finished qdiffx linear iterations at : 15:14:31 total time elapsed so far: 5.770000 # loops : 50 mean,max change (kT/e) : 5.3920361E-05 6.0443878E-03 energy calculations done at 5.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.940000 DelPhi exited at 15:14:32 5.948u 0.428s 0:08.05 79.0% 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 15 2011 at 15:14:32 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: 388 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: SEP 250 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.825641 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): -7.791000 50.70900 ymin,ymax (A): 7.296999 61.76500 zmin,zma (A): 1.057000 55.92100 x,y,z range (A): 58.50000 54.46800 54.86400 scale (grids/A): 1.825641 object centre (A): 21.45900 34.53100 28.48900 number of atom coordinates read : 2809 total number of charged atoms : 2599 net assigned charge : 6.039018 assigned positive charge : 418.8239 centred at (gu) : 90.82176 92.85252 92.80957 assigned negative charge : -412.7853 centred at (gu) : 91.66870 92.47472 92.29451 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 71342 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23883 grid for indexing accessible points = 1.400000 m= 26746 mr = 48752 m= 4726 mr = 19563 m= 237 mr = 2986 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 31698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20371 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) : 0.6085470 object centre at (A) : 21.45900 34.53100 28.48900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2681441E-03 7.0720270E-02 midg,1,midg; midg,igrid,midg -1.8776054E-02 4.7254621E-04 1,midg,midg; igrid,midg,midg 5.9894629E-02 -5.5758420E-02 gauss-seidel spectral radius is 0.9985397 estimated iterations to convergence 207 setup time was (sec) 1.000000 now iterating at: 15:14:34 rms-change max change #iterations 4.082768 181.2353 at 10iterations 1.858347 77.98992 at 20iterations 0.8475500 30.22665 at 30iterations 0.3873634 12.62542 at 40iterations 0.1767485 5.857807 at 50iterations 8.0804586E-02 2.687515 at 60iterations 3.7018582E-02 1.353228 at 70iterations 1.6862407E-02 0.5360603 at 80iterations 7.7194674E-03 0.2430348 at 90iterations 3.5451360E-03 0.1160583 at 100iterations 1.6315755E-03 5.3365231E-02 at 110iterations 7.6543749E-04 2.4557114E-02 at 120iterations finished qdiffx linear iterations at : 15:14:52 total time elapsed so far: 13.77000 # loops : 120 mean,max change (kT/e) : 7.6543749E-04 2.4557114E-02 energy calculations done at 13.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.94000 DelPhi exited at 15:14:53 13.940u 0.546s 0:20.96 69.0% 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 15 2011 at 15:14:53 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: 388 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: SEP 250 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.738461 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): -7.791000 50.70900 ymin,ymax (A): 7.296999 61.76500 zmin,zma (A): 1.057000 55.92100 x,y,z range (A): 58.50000 54.46800 54.86400 scale (grids/A): 2.738461 object centre (A): 21.45900 34.53100 28.48900 number of atom coordinates read : 2809 total number of charged atoms : 2599 net assigned charge : 6.039018 assigned positive charge : 418.8239 centred at (gu) : 91.23243 94.27857 94.21420 assigned negative charge : -412.7853 centred at (gu) : 92.50303 93.71198 93.44168 start vw surface at 0.1200000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 164383 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23883 grid for indexing accessible points = 1.400000 m= 84642 mr = 118076 m= 33143 mr = 68718 m= 8440 mr = 26578 m= 1106 mr = 6310 m= 52 mr = 668 m= 0 mr = 5 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.690000 number of dielectric boundary points 71411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 20782 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) : 1.825641 object centre at (A) : 21.45900 34.53100 28.48900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1342221 0.9951273 midg,1,midg; midg,igrid,midg -0.2781314 -0.1238229 1,midg,midg; igrid,midg,midg 1.094322 -0.8155129 gauss-seidel spectral radius is 0.9992356 estimated iterations to convergence 286 setup time was (sec) 2.090000 now iterating at: 15:14:57 rms-change max change #iterations 9.826664 376.8773 at 10iterations 5.753936 144.8563 at 20iterations 3.335737 101.2929 at 30iterations 1.929702 42.02192 at 40iterations 1.114388 21.73274 at 50iterations 0.6395841 11.61291 at 60iterations 0.3673452 7.305893 at 70iterations 0.2105419 4.129303 at 80iterations 0.1204714 2.313761 at 90iterations 6.8847999E-02 1.386250 at 100iterations 3.9396290E-02 0.8022385 at 110iterations 2.2512773E-02 0.4629645 at 120iterations 1.2832804E-02 0.2382298 at 130iterations 7.3438585E-03 0.1361208 at 140iterations 4.1935034E-03 8.3677292E-02 at 150iterations 2.3943603E-03 5.1017761E-02 at 160iterations 1.3719444E-03 2.7954102E-02 at 170iterations 7.9178956E-04 1.5588760E-02 at 180iterations finished qdiffx linear iterations at : 15:15:27 total time elapsed so far: 23.41000 # loops : 180 mean,max change (kT/e) : 7.9178956E-04 1.5588760E-02 energy calculations done at 23.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.58000 DelPhi exited at 15:15:27 23.582u 0.605s 0:34.41 70.2% 0+0k 0+0io 0pf+0w