Tue Oct 11 06:07:45 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 Tue Oct 11 2011 at 06:07:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7011324 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): 6.583000 50.89300 ymin,ymax (A): 16.99100 57.79300 zmin,zma (A): -2.599000 48.17600 x,y,z range (A): 44.31000 40.80200 50.77500 scale (grids/A): 0.7011324 object centre (A): 28.73800 37.39200 22.78850 number of atom coordinates read : 2053 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 90.34428 89.73276 89.86845 assigned negative charge : -304.2972 centred at (gu) : 90.16612 89.75980 89.89590 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6811 nv = 96 ne = 84 npr = 41468 no. pairs analyzed = 41468 no. exposed pairs = 2489 no. arc points = 17039 no. surface atoms = 853 nbur = 1200 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 3899 m= 7 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1587 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7608 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7324386E-08 4.1632600E-08 midg,1,midg; midg,igrid,midg 6.8918958E-08 4.0760295E-08 1,midg,midg; igrid,midg,midg -2.0086253E-08 1.3637744E-07 gauss-seidel spectral radius is 0.9893940 estimated iterations to convergence 79 setup time was (sec) 0.3600000 now iterating at: 06:07:45 rms-change max change #iterations 0.1904508 28.91583 at 10iterations 2.3540191E-02 3.518857 at 20iterations 2.9402783E-03 0.3879681 at 30iterations 4.3927354E-04 5.6930542E-02 at 40iterations 9.7571676E-05 1.2704849E-02 at 50iterations finished qdiffx linear iterations at : 06:07:48 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 9.7571676E-05 1.2704849E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 06:07:49 3.340u 0.171s 0:04.15 84.5% 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 06:07:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.103397 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): 6.583000 50.89300 ymin,ymax (A): 16.99100 57.79300 zmin,zma (A): -2.599000 48.17600 x,y,z range (A): 44.31000 40.80200 50.77500 scale (grids/A): 2.103397 object centre (A): 28.73800 37.39200 22.78850 number of atom coordinates read : 2053 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 91.03276 89.19801 89.60537 assigned negative charge : -304.2972 centred at (gu) : 90.49852 89.27934 89.68790 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72254 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17039 grid for indexing accessible points = 1.400000 m= 28295 mr = 51114 m= 5349 mr = 21171 m= 476 mr = 3451 m= 13 mr = 212 m= 0 mr = 3 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 30436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15320 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) : 0.7011324 object centre at (A) : 28.73800 37.39200 22.78850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2597214E-02 5.3926583E-02 midg,1,midg; midg,igrid,midg 2.9893752E-02 3.4482321E-03 1,midg,midg; igrid,midg,midg 1.3886866E-02 4.5262530E-02 gauss-seidel spectral radius is 0.9988105 estimated iterations to convergence 230 setup time was (sec) 0.5800000 now iterating at: 06:07:50 rms-change max change #iterations 4.453065 180.2747 at 10iterations 2.185703 71.00146 at 20iterations 1.074213 33.97916 at 30iterations 0.5334429 15.98956 at 40iterations 0.2627622 8.739854 at 50iterations 0.1295234 3.864500 at 60iterations 6.4095929E-02 1.933059 at 70iterations 3.1610817E-02 0.9109459 at 80iterations 1.5667565E-02 0.4936848 at 90iterations 7.7748373E-03 0.2533321 at 100iterations 3.8736181E-03 0.1334381 at 110iterations 1.9618243E-03 6.3081741E-02 at 120iterations finished qdiffx linear iterations at : 06:07:57 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 1.9618243E-03 6.3081741E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 06:07:57 7.735u 0.207s 0:08.37 94.7% 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 Tue Oct 11 2011 at 06:07:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.155096 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): 6.583000 50.89300 ymin,ymax (A): 16.99100 57.79300 zmin,zma (A): -2.599000 48.17600 x,y,z range (A): 44.31000 40.80200 50.77500 scale (grids/A): 3.155096 object centre (A): 28.73800 37.39200 22.78850 number of atom coordinates read : 2053 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 91.54916 88.79703 89.40805 assigned negative charge : -304.2972 centred at (gu) : 90.74783 88.91908 89.53187 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 166591 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17039 grid for indexing accessible points = 1.400000 m= 89078 mr = 123198 m= 35144 mr = 73717 m= 9938 mr = 28430 m= 1876 mr = 7507 m= 199 mr = 1294 m= 5 mr = 112 m= 0 mr = 2 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.110000 number of dielectric boundary points 68571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 15428 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) : 2.103397 object centre at (A) : 28.73800 37.39200 22.78850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4557833 0.4888456 midg,1,midg; midg,igrid,midg 0.2285374 3.3699926E-05 1,midg,midg; igrid,midg,midg 0.2154728 0.3474607 gauss-seidel spectral radius is 0.9992893 estimated iterations to convergence 296 setup time was (sec) 1.350000 now iterating at: 06:07:59 rms-change max change #iterations 9.981851 318.7854 at 10iterations 5.888894 137.1287 at 20iterations 3.474485 72.87415 at 30iterations 2.043014 42.84379 at 40iterations 1.201127 24.97981 at 50iterations 0.7036992 13.69126 at 60iterations 0.4127264 7.721571 at 70iterations 0.2413978 4.627175 at 80iterations 0.1409332 2.840300 at 90iterations 8.2564771E-02 1.559979 at 100iterations 4.8265878E-02 0.8223038 at 110iterations 2.8282193E-02 0.5186586 at 120iterations 1.6668873E-02 0.2925682 at 130iterations 9.8936642E-03 0.1771812 at 140iterations 5.9702089E-03 0.1053734 at 150iterations 3.6765360E-03 7.5464249E-02 at 160iterations 2.3700676E-03 4.5608521E-02 at 170iterations 1.6014298E-03 3.2440186E-02 at 180iterations finished qdiffx linear iterations at : 06:08:10 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 1.6014298E-03 3.2440186E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 06:08:11 12.732u 0.211s 0:13.61 95.0% 0+0k 0+0io 0pf+0w