Tue Oct 11 08:25:09 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 08:25:09 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2768 !!! WARNING: ILE 30 has a net charge of 0.5000 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6464617 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): -12.23600 36.34300 ymin,ymax (A): -27.13600 21.56800 zmin,zma (A): -9.543000 45.52600 x,y,z range (A): 48.57900 48.70400 55.06900 scale (grids/A): 0.6464617 object centre (A): 12.05350 -2.784000 17.99150 number of atom coordinates read : 2768 total number of charged atoms : 2616 net assigned charge : 5.662015 assigned positive charge : 416.3838 centred at (gu) : 90.55345 90.55459 91.73869 assigned negative charge : -410.7224 centred at (gu) : 90.31563 90.36968 91.72453 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7642 nv = 96 ne = 84 npr = 57357 no. pairs analyzed = 57357 no. exposed pairs = 3157 no. arc points = 21966 no. surface atoms = 1069 nbur = 1699 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 387 mr = 4451 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3200000 number of dielectric boundary points 3520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2238 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9272 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2663660E-09 1.6651349E-08 midg,1,midg; midg,igrid,midg -1.6015656E-08 4.0607105E-08 1,midg,midg; igrid,midg,midg -2.3219540E-08 4.8945921E-08 gauss-seidel spectral radius is 0.9876085 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 08:25:10 rms-change max change #iterations 0.1566947 22.72141 at 10iterations 1.6194759E-02 2.077257 at 20iterations 1.6772717E-03 0.2194633 at 30iterations 1.9998959E-04 2.4898529E-02 at 40iterations 3.5444951E-05 6.5002441E-03 at 50iterations finished qdiffx linear iterations at : 08:25:13 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 3.5444951E-05 6.5002441E-03 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 08:25:14 4.428u 0.414s 0:05.33 90.6% 0+0k 0+0io 1pf+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 08:25:14 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2768 !!! WARNING: ILE 30 has a net charge of 0.5000 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.939385 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): -12.23600 36.34300 ymin,ymax (A): -27.13600 21.56800 zmin,zma (A): -9.543000 45.52600 x,y,z range (A): 48.57900 48.70400 55.06900 scale (grids/A): 1.939385 object centre (A): 12.05350 -2.784000 17.99150 number of atom coordinates read : 2768 total number of charged atoms : 2616 net assigned charge : 5.662015 assigned positive charge : 416.3838 centred at (gu) : 91.65998 91.66328 95.21549 assigned negative charge : -410.7224 centred at (gu) : 90.94651 91.10887 95.17350 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 82353 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21966 grid for indexing accessible points = 1.400000 m= 30956 mr = 59084 m= 5012 mr = 23615 m= 317 mr = 3378 m= 7 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 999 time to turn everything in is 0.6600000 number of dielectric boundary points 32443 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 20574 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) : 0.6464617 object centre at (A) : 12.05350 -2.784000 17.99150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4223563E-02 1.5431673E-02 midg,1,midg; midg,igrid,midg -1.2552721E-02 3.0265506E-02 1,midg,midg; igrid,midg,midg -3.0689249E-03 6.7522109E-02 gauss-seidel spectral radius is 0.9986910 estimated iterations to convergence 219 setup time was (sec) 1.030000 now iterating at: 08:25:16 rms-change max change #iterations 4.534128 211.8976 at 10iterations 2.168063 76.10625 at 20iterations 1.033199 32.99652 at 30iterations 0.4915042 14.71963 at 40iterations 0.2339725 6.930792 at 50iterations 0.1119909 3.504345 at 60iterations 5.3425621E-02 1.586796 at 70iterations 2.5439447E-02 0.8472013 at 80iterations 1.2151401E-02 0.3533325 at 90iterations 5.7943049E-03 0.1690187 at 100iterations 2.7759015E-03 8.8675618E-02 at 110iterations 1.3256301E-03 4.3579102E-02 at 120iterations finished qdiffx linear iterations at : 08:25:25 total time elapsed so far: 10.78000 # loops : 120 mean,max change (kT/e) : 1.3256301E-03 4.3579102E-02 energy calculations done at 10.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.97000 DelPhi exited at 08:25:26 10.970u 0.431s 0:11.85 96.2% 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 08:25:26 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2768 !!! WARNING: ILE 30 has a net charge of 0.5000 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.909078 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): -12.23600 36.34300 ymin,ymax (A): -27.13600 21.56800 zmin,zma (A): -9.543000 45.52600 x,y,z range (A): 48.57900 48.70400 55.06900 scale (grids/A): 2.909078 object centre (A): 12.05350 -2.784000 17.99150 number of atom coordinates read : 2768 total number of charged atoms : 2616 net assigned charge : 5.662015 assigned positive charge : 416.3838 centred at (gu) : 92.48973 92.49473 97.82309 assigned negative charge : -410.7224 centred at (gu) : 91.41953 91.66312 97.76012 start vw surface at 0.1200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 190251 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21966 grid for indexing accessible points = 1.400000 m= 99662 mr = 142197 m= 37028 mr = 83352 m= 9242 mr = 30621 m= 1451 mr = 7220 m= 116 mr = 1053 m= 4 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 3530 time to turn everything in is 1.750000 number of dielectric boundary points 73241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 20926 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) : 1.939385 object centre at (A) : 12.05350 -2.784000 17.99150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3380427 0.3238578 midg,1,midg; midg,igrid,midg -0.1411351 0.3573045 1,midg,midg; igrid,midg,midg -2.7831795E-02 0.5747045 gauss-seidel spectral radius is 0.9992689 estimated iterations to convergence 292 setup time was (sec) 2.080000 now iterating at: 08:25:29 rms-change max change #iterations 10.50018 426.0675 at 10iterations 6.145077 130.2754 at 20iterations 3.584261 71.46208 at 30iterations 2.084941 42.39332 at 40iterations 1.211596 21.14655 at 50iterations 0.7025515 12.79178 at 60iterations 0.4066142 7.102689 at 70iterations 0.2356180 4.025688 at 80iterations 0.1364988 2.580191 at 90iterations 7.8988701E-02 1.545861 at 100iterations 4.5605674E-02 0.8233109 at 110iterations 2.6369061E-02 0.4560890 at 120iterations 1.5209364E-02 0.2494049 at 130iterations 8.8073174E-03 0.1497192 at 140iterations 5.0980933E-03 8.5374832E-02 at 150iterations 2.9554975E-03 5.1116943E-02 at 160iterations 1.7178701E-03 2.8753281E-02 at 170iterations 1.0053425E-03 1.6739845E-02 at 180iterations finished qdiffx linear iterations at : 08:25:45 total time elapsed so far: 18.37000 # loops : 180 mean,max change (kT/e) : 1.0053425E-03 1.6739845E-02 energy calculations done at 18.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.54000 DelPhi exited at 08:25:46 18.543u 0.480s 0:19.43 97.8% 0+0k 0+0io 0pf+0w