Tue Oct 11 03:15:19 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 03:15:19 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3690 !!! WARNING: HIR 424 has a net charge of 0.5140 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: 0.5288333 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): 37.19600 94.56900 ymin,ymax (A): 20.73600 72.84000 zmin,zma (A): -8.743999 58.57400 x,y,z range (A): 57.37300 52.10400 67.31800 scale (grids/A): 0.5288333 object centre (A): 65.88250 46.78800 24.91500 number of atom coordinates read : 3690 total number of charged atoms : 3536 net assigned charge : -6.985975 assigned positive charge : 568.9668 centred at (gu) : 89.30611 89.33871 90.72483 assigned negative charge : -575.9556 centred at (gu) : 89.33335 89.31687 90.76707 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6788 nv = 96 ne = 84 npr = 70864 no. pairs analyzed = 70864 no. exposed pairs = 5237 no. arc points = 38098 no. surface atoms = 1716 nbur = 1974 mkacc time = 0.1800000 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= 269 mr = 3099 m= 0 mr = 9 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3745 ## 502 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8991 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6186428E-11 -4.8633558E-10 midg,1,midg; midg,igrid,midg -3.7008091E-10 -1.0217077E-10 1,midg,midg; igrid,midg,midg -1.1248903E-10 -2.8352648E-10 gauss-seidel spectral radius is 0.9816487 estimated iterations to convergence 61 setup time was (sec) 0.6800000 now iterating at: 03:15:20 rms-change max change #iterations 7.0265867E-02 11.71087 at 10iterations 4.3041459E-03 0.6507506 at 20iterations 2.6064110E-04 4.3775558E-02 at 30iterations 1.5963000E-05 2.5806427E-03 at 40iterations 1.0213901E-06 1.5640259E-04 at 50iterations finished qdiffx linear iterations at : 03:15:24 total time elapsed so far: 4.530000 # loops : 50 mean,max change (kT/e) : 1.0213901E-06 1.5640259E-04 energy calculations done at 4.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.700000 DelPhi exited at 03:15:24 4.703u 0.395s 0:05.65 90.0% 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 Tue Oct 11 2011 at 03:15:25 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3690 !!! WARNING: HIR 424 has a net charge of 0.5140 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: 1.586500 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): 37.19600 94.56900 ymin,ymax (A): 20.73600 72.84000 zmin,zma (A): -8.743999 58.57400 x,y,z range (A): 57.37300 52.10400 67.31800 scale (grids/A): 1.586500 object centre (A): 65.88250 46.78800 24.91500 number of atom coordinates read : 3690 total number of charged atoms : 3536 net assigned charge : -6.985975 assigned positive charge : 568.9668 centred at (gu) : 87.91719 88.01459 92.17294 assigned negative charge : -575.9556 centred at (gu) : 87.99986 87.95007 92.30079 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75315 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38098 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 21855 mr = 47811 m= 2088 mr = 13847 m= 49 mr = 842 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 36807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 437 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 26859 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) : 0.5288333 object centre at (A) : 65.88250 46.78800 24.91500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7352041E-02 -7.5246873E-03 midg,1,midg; midg,igrid,midg -7.0132953E-03 -8.8730529E-03 1,midg,midg; igrid,midg,midg 9.4166324E-03 -7.9144472E-03 gauss-seidel spectral radius is 0.9981803 estimated iterations to convergence 186 setup time was (sec) 0.9800000 now iterating at: 03:15:26 rms-change max change #iterations 3.622847 173.5990 at 10iterations 1.497603 55.32473 at 20iterations 0.6214859 21.68150 at 30iterations 0.2591194 9.466102 at 40iterations 0.1072834 4.032965 at 50iterations 4.4695880E-02 1.635436 at 60iterations 1.8575642E-02 0.6274948 at 70iterations 7.7259759E-03 0.2642865 at 80iterations 3.2183826E-03 0.1190414 at 90iterations 1.3407657E-03 4.6623230E-02 at 100iterations 5.5716914E-04 1.9398689E-02 at 110iterations 2.3233901E-04 7.6446533E-03 at 120iterations finished qdiffx linear iterations at : 03:15:36 total time elapsed so far: 10.86000 # loops : 120 mean,max change (kT/e) : 2.3233901E-04 7.6446533E-03 energy calculations done at 10.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.04000 DelPhi exited at 03:15:36 11.040u 0.433s 0:11.88 96.5% 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 03:15:36 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3690 !!! WARNING: HIR 424 has a net charge of 0.5140 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: 2.379750 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): 37.19600 94.56900 ymin,ymax (A): 20.73600 72.84000 zmin,zma (A): -8.743999 58.57400 x,y,z range (A): 57.37300 52.10400 67.31800 scale (grids/A): 2.379750 object centre (A): 65.88250 46.78800 24.91500 number of atom coordinates read : 3690 total number of charged atoms : 3536 net assigned charge : -6.985975 assigned positive charge : 568.9668 centred at (gu) : 86.87554 87.02184 93.25919 assigned negative charge : -575.9556 centred at (gu) : 86.99960 86.92510 93.45105 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 175103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38098 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 75542 mr = 118635 m= 20862 mr = 56608 m= 3035 mr = 14690 m= 148 mr = 1669 m= 4 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.520000 number of dielectric boundary points 83064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 28237 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) : 1.586500 object centre at (A) : 65.88250 46.78800 24.91500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5935835 8.6292811E-02 midg,1,midg; midg,igrid,midg -0.1085579 -0.1310197 1,midg,midg; igrid,midg,midg 0.1901232 -0.1010958 gauss-seidel spectral radius is 0.9991775 estimated iterations to convergence 275 setup time was (sec) 1.880000 now iterating at: 03:15:39 rms-change max change #iterations 9.842954 382.3401 at 10iterations 5.686811 154.1807 at 20iterations 3.259525 98.96844 at 30iterations 1.855427 51.13147 at 40iterations 1.054245 23.00673 at 50iterations 0.5940631 13.54374 at 60iterations 0.3344283 8.057337 at 70iterations 0.1883134 3.875942 at 80iterations 0.1055732 2.273304 at 90iterations 5.9240568E-02 1.215438 at 100iterations 3.3080056E-02 0.6741028 at 110iterations 1.8520694E-02 0.4108257 at 120iterations 1.0341466E-02 0.2324829 at 130iterations 5.7825670E-03 0.1103764 at 140iterations 3.2310304E-03 7.3852539E-02 at 150iterations 1.7991762E-03 3.6582947E-02 at 160iterations 1.0057411E-03 2.0298004E-02 at 170iterations 5.6040828E-04 1.1428118E-02 at 180iterations finished qdiffx linear iterations at : 03:15:56 total time elapsed so far: 18.83000 # loops : 180 mean,max change (kT/e) : 5.6040828E-04 1.1428118E-02 energy calculations done at 18.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.00000 DelPhi exited at 03:15:57 19.003u 0.456s 0:20.21 96.2% 0+0k 0+0io 0pf+0w