Sun Oct 9 10:34:48 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 Sun Oct 9 2011 at 10:34:48 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2890 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: CME 219 has a net charge of -0.3480 !!! WARNING: CME 313 has a net charge of -0.3480 !!! WARNING: CME 452 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 0.5812530 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): -45.25800 15.98900 ymin,ymax (A): -26.72100 22.29300 zmin,zma (A): -28.18900 27.19700 x,y,z range (A): 61.24700 49.01400 55.38600 scale (grids/A): 0.5812530 object centre (A): -14.63450 -2.214000 -0.4959993 number of atom coordinates read : 2890 total number of charged atoms : 2788 net assigned charge : 1.933026 assigned positive charge : 428.0631 centred at (gu) : 88.28061 91.33570 91.53668 assigned negative charge : -426.1318 centred at (gu) : 88.22682 91.27296 91.45867 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6766 nv = 96 ne = 84 npr = 56297 no. pairs analyzed = 56297 no. exposed pairs = 3965 no. arc points = 27475 no. surface atoms = 1315 nbur = 1575 mkacc time = 9.9999994E-02 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 = 1.484000 m= 377 mr = 3456 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2743 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8448 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.0375429E-10 3.0224054E-09 midg,1,midg; midg,igrid,midg -7.0101874E-10 2.4291309E-09 1,midg,midg; igrid,midg,midg -1.1774699E-09 1.0582822E-09 gauss-seidel spectral radius is 0.9847275 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 10:34:48 rms-change max change #iterations 9.5814623E-02 13.98661 at 10iterations 7.7389348E-03 1.071574 at 20iterations 8.2250283E-04 0.1314220 at 30iterations 1.6444028E-04 2.5984287E-02 at 40iterations 4.4209391E-05 6.9746971E-03 at 50iterations finished qdiffx linear iterations at : 10:34:51 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 4.4209391E-05 6.9746971E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 10:34:52 3.387u 0.182s 0:03.97 89.6% 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 Sun Oct 9 2011 at 10:34:52 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2890 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: CME 219 has a net charge of -0.3480 !!! WARNING: CME 313 has a net charge of -0.3480 !!! WARNING: CME 452 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 1.743759 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): -45.25800 15.98900 ymin,ymax (A): -26.72100 22.29300 zmin,zma (A): -28.18900 27.19700 x,y,z range (A): 61.24700 49.01400 55.38600 scale (grids/A): 1.743759 object centre (A): -14.63450 -2.214000 -0.4959993 number of atom coordinates read : 2890 total number of charged atoms : 2788 net assigned charge : 1.933026 assigned positive charge : 428.0631 centred at (gu) : 84.84068 94.00604 94.60925 assigned negative charge : -426.1318 centred at (gu) : 84.68036 93.81882 94.37595 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73410 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27475 grid for indexing accessible points = 1.400000 m= 25798 mr = 49385 m= 3888 mr = 17913 m= 175 mr = 2132 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 33816 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 21676 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) : 0.5812530 object centre at (A) : -14.63450 -2.214000 -0.4959993 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6264250E-03 1.0400821E-02 midg,1,midg; midg,igrid,midg 5.4244637E-03 2.3714811E-02 1,midg,midg; igrid,midg,midg -4.5414567E-03 4.1120821E-03 gauss-seidel spectral radius is 0.9984238 estimated iterations to convergence 200 setup time was (sec) 0.5800000 now iterating at: 10:34:53 rms-change max change #iterations 3.730157 194.7914 at 10iterations 1.644566 54.31557 at 20iterations 0.7283486 25.29186 at 30iterations 0.3217646 10.91301 at 40iterations 0.1424592 4.708295 at 50iterations 6.3075840E-02 1.950975 at 60iterations 2.7920412E-02 0.9382629 at 70iterations 1.2371543E-02 0.4368992 at 80iterations 5.5300267E-03 0.2048740 at 90iterations 2.4919009E-03 8.3057404E-02 at 100iterations 1.1395380E-03 3.6741257E-02 at 110iterations 5.3615257E-04 1.7666817E-02 at 120iterations finished qdiffx linear iterations at : 10:35:00 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 5.3615257E-04 1.7666817E-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 10:35:00 7.728u 0.196s 0:08.25 95.8% 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 Sun Oct 9 2011 at 10:35:00 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2890 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: CME 219 has a net charge of -0.3480 !!! WARNING: CME 313 has a net charge of -0.3480 !!! WARNING: CME 452 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 2.615638 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): -45.25800 15.98900 ymin,ymax (A): -26.72100 22.29300 zmin,zma (A): -28.18900 27.19700 x,y,z range (A): 61.24700 49.01400 55.38600 scale (grids/A): 2.615638 object centre (A): -14.63450 -2.214000 -0.4959993 number of atom coordinates read : 2890 total number of charged atoms : 2788 net assigned charge : 1.933026 assigned positive charge : 428.0631 centred at (gu) : 82.26091 96.00895 96.91368 assigned negative charge : -426.1318 centred at (gu) : 82.02063 95.72813 96.56385 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 169939 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27475 grid for indexing accessible points = 1.400000 m= 83320 mr = 120913 m= 29746 mr = 65575 m= 6764 mr = 22714 m= 743 mr = 4684 m= 22 mr = 374 m= 0 mr = 3 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 76271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 22297 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) : 1.743759 object centre at (A) : -14.63450 -2.214000 -0.4959993 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8135617E-02 0.1355560 midg,1,midg; midg,igrid,midg 0.1157011 0.3122186 1,midg,midg; igrid,midg,midg -2.3516187E-02 0.1204483 gauss-seidel spectral radius is 0.9992101 estimated iterations to convergence 281 setup time was (sec) 1.150000 now iterating at: 10:35:01 rms-change max change #iterations 9.399455 264.5717 at 10iterations 5.480247 176.8539 at 20iterations 3.155497 72.31053 at 30iterations 1.814640 37.35297 at 40iterations 1.041655 20.92759 at 50iterations 0.5950407 11.29353 at 60iterations 0.3388400 6.714531 at 70iterations 0.1925791 3.611586 at 80iterations 0.1092010 2.150467 at 90iterations 6.1867107E-02 1.198788 at 100iterations 3.5094649E-02 0.7289200 at 110iterations 1.9934829E-02 0.4015198 at 120iterations 1.1294027E-02 0.2140808 at 130iterations 6.4285020E-03 0.1284094 at 140iterations 3.6680172E-03 6.8085670E-02 at 150iterations 2.1100428E-03 3.9766312E-02 at 160iterations 1.2308125E-03 2.2615433E-02 at 170iterations 7.3470036E-04 1.4621735E-02 at 180iterations finished qdiffx linear iterations at : 10:35:13 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 7.3470036E-04 1.4621735E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 10:35:13 12.600u 0.211s 0:13.11 97.7% 0+0k 0+0io 0pf+0w