Sat Oct 8 15:46:34 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 Sat Oct 8 2011 at 15:46:34 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 = 2300 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6596379 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): -17.70000 30.51900 ymin,ymax (A): 3.512000 48.23600 zmin,zma (A): -16.87700 37.09200 x,y,z range (A): 48.21900 44.72400 53.96900 scale (grids/A): 0.6596379 object centre (A): 6.409500 25.87400 10.10750 number of atom coordinates read : 2300 total number of charged atoms : 2235 net assigned charge : 4.500012 assigned positive charge : 343.4932 centred at (gu) : 89.35658 91.64891 89.87426 assigned negative charge : -338.9938 centred at (gu) : 89.31021 91.57092 89.94978 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6788 nv = 96 ne = 84 npr = 46096 no. pairs analyzed = 46096 no. exposed pairs = 2942 no. arc points = 20169 no. surface atoms = 1010 nbur = 1290 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 3729 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.2700000 number of dielectric boundary points 3400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1969 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8053 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4518343E-08 -1.8337944E-09 midg,1,midg; midg,igrid,midg -1.4902870E-09 3.4309554E-08 1,midg,midg; igrid,midg,midg 3.5032122E-09 1.6635504E-08 gauss-seidel spectral radius is 0.9880630 estimated iterations to convergence 75 setup time was (sec) 0.5500000 now iterating at: 15:46:35 rms-change max change #iterations 0.1564383 28.50430 at 10iterations 1.6468437E-02 2.362898 at 20iterations 1.8060245E-03 0.2463779 at 30iterations 2.2455207E-04 3.7992477E-02 at 40iterations 4.1084630E-05 5.5885315E-03 at 50iterations finished qdiffx linear iterations at : 15:46:38 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 4.1084630E-05 5.5885315E-03 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 15:46:39 4.267u 0.277s 0:04.80 94.3% 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 15:46:39 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 = 2300 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.978914 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): -17.70000 30.51900 ymin,ymax (A): 3.512000 48.23600 zmin,zma (A): -16.87700 37.09200 x,y,z range (A): 48.21900 44.72400 53.96900 scale (grids/A): 1.978914 object centre (A): 6.409500 25.87400 10.10750 number of atom coordinates read : 2300 total number of charged atoms : 2235 net assigned charge : 4.500012 assigned positive charge : 343.4932 centred at (gu) : 88.06970 94.94625 89.62226 assigned negative charge : -338.9938 centred at (gu) : 87.93044 94.71291 89.84923 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20169 grid for indexing accessible points = 1.400000 m= 26960 mr = 51068 m= 4598 mr = 19809 m= 299 mr = 2936 m= 10 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 166 time to turn everything in is 0.5500000 number of dielectric boundary points 31225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17647 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) : 0.6596379 object centre at (A) : 6.409500 25.87400 10.10750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4708711E-02 -6.7757056E-03 midg,1,midg; midg,igrid,midg -2.0265540E-03 3.2162238E-02 1,midg,midg; igrid,midg,midg -3.6921103E-02 2.1254791E-02 gauss-seidel spectral radius is 0.9987031 estimated iterations to convergence 220 setup time was (sec) 0.8800000 now iterating at: 15:46:40 rms-change max change #iterations 4.236095 182.6245 at 10iterations 2.025394 77.27542 at 20iterations 0.9666288 32.53008 at 30iterations 0.4603290 14.03687 at 40iterations 0.2203772 7.118512 at 50iterations 0.1056579 3.123547 at 60iterations 5.0450020E-02 1.536074 at 70iterations 2.4117295E-02 0.7444096 at 80iterations 1.1476525E-02 0.3425913 at 90iterations 5.5219536E-03 0.1750336 at 100iterations 2.6374566E-03 8.5273743E-02 at 110iterations 1.2694076E-03 3.8817406E-02 at 120iterations finished qdiffx linear iterations at : 15:46:49 total time elapsed so far: 9.410000 # loops : 120 mean,max change (kT/e) : 1.2694076E-03 3.8817406E-02 energy calculations done at 9.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 15:46:49 9.590u 0.281s 0:10.13 97.4% 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 15:46:49 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 = 2300 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.968371 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): -17.70000 30.51900 ymin,ymax (A): 3.512000 48.23600 zmin,zma (A): -16.87700 37.09200 x,y,z range (A): 48.21900 44.72400 53.96900 scale (grids/A): 2.968371 object centre (A): 6.409500 25.87400 10.10750 number of atom coordinates read : 2300 total number of charged atoms : 2235 net assigned charge : 4.500012 assigned positive charge : 343.4932 centred at (gu) : 87.10439 97.41924 89.43324 assigned negative charge : -338.9938 centred at (gu) : 86.89565 97.06923 89.77377 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 169573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20169 grid for indexing accessible points = 1.400000 m= 86302 mr = 123702 m= 32438 mr = 70508 m= 8574 mr = 26119 m= 1388 mr = 6552 m= 100 mr = 924 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 588 time to turn everything in is 1.480000 number of dielectric boundary points 70522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 17880 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) : 1.978914 object centre at (A) : 6.409500 25.87400 10.10750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2424449 -0.1674485 midg,1,midg; midg,igrid,midg -4.5737937E-02 0.2735577 1,midg,midg; igrid,midg,midg -0.5436065 0.2146880 gauss-seidel spectral radius is 0.9992778 estimated iterations to convergence 294 setup time was (sec) 1.830000 now iterating at: 15:46:51 rms-change max change #iterations 9.890260 426.6291 at 10iterations 5.817394 130.9456 at 20iterations 3.419638 76.69614 at 30iterations 2.008744 39.06712 at 40iterations 1.174320 21.85257 at 50iterations 0.6874297 12.50892 at 60iterations 0.3999957 7.019590 at 70iterations 0.2324855 4.497205 at 80iterations 0.1351961 2.799566 at 90iterations 7.8583822E-02 1.718305 at 100iterations 4.5608714E-02 0.8016613 at 110iterations 2.6450446E-02 0.4760590 at 120iterations 1.5326433E-02 0.2726436 at 130iterations 8.9007709E-03 0.1628370 at 140iterations 5.1650596E-03 9.8147392E-02 at 150iterations 3.0023425E-03 5.6509435E-02 at 160iterations 1.7441219E-03 3.3812523E-02 at 170iterations 1.0165405E-03 1.8878937E-02 at 180iterations finished qdiffx linear iterations at : 15:47:04 total time elapsed so far: 15.10000 # loops : 180 mean,max change (kT/e) : 1.0165405E-03 1.8878937E-02 energy calculations done at 15.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.29000 DelPhi exited at 15:47:05 15.289u 0.259s 0:15.80 98.2% 0+0k 0+0io 0pf+0w