Tue Oct 11 05:29:49 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 05:29:49 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2277 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: 0.6866357 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): 19.77000 63.16300 ymin,ymax (A): -3.556000 33.71800 zmin,zma (A): 20.02400 71.87100 x,y,z range (A): 43.39300 37.27400 51.84700 scale (grids/A): 0.6866357 object centre (A): 41.46650 15.08100 45.94750 number of atom coordinates read : 2277 total number of charged atoms : 1957 net assigned charge : 6.500009 assigned positive charge : 316.7440 centred at (gu) : 90.02894 89.60878 89.19724 assigned negative charge : -310.2442 centred at (gu) : 90.16460 89.63905 89.14819 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6685 nv = 96 ne = 84 npr = 41670 no. pairs analyzed = 41670 no. exposed pairs = 2553 no. arc points = 17324 no. surface atoms = 871 nbur = 1406 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 399 mr = 3851 m= 2 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1685 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7530 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1057364E-08 4.1059319E-08 midg,1,midg; midg,igrid,midg 4.5759641E-08 2.2234579E-08 1,midg,midg; igrid,midg,midg 7.3525300E-08 -8.7973104E-09 gauss-seidel spectral radius is 0.9889494 estimated iterations to convergence 78 setup time was (sec) 0.3500000 now iterating at: 05:29:49 rms-change max change #iterations 0.1732059 26.40507 at 10iterations 2.0455096E-02 2.771458 at 20iterations 2.4609901E-03 0.3487082 at 30iterations 3.6712977E-04 5.0501823E-02 at 40iterations 8.5567139E-05 1.0950089E-02 at 50iterations finished qdiffx linear iterations at : 05:29:52 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 8.5567139E-05 1.0950089E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 05:29:52 3.403u 0.187s 0:03.95 90.6% 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 Tue Oct 11 2011 at 05:29:53 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2277 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: 2.059907 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): 19.77000 63.16300 ymin,ymax (A): -3.556000 33.71800 zmin,zma (A): 20.02400 71.87100 x,y,z range (A): 43.39300 37.27400 51.84700 scale (grids/A): 2.059907 object centre (A): 41.46650 15.08100 45.94750 number of atom coordinates read : 2277 total number of charged atoms : 1957 net assigned charge : 6.500009 assigned positive charge : 316.7440 centred at (gu) : 90.08691 88.82631 87.59170 assigned negative charge : -310.2442 centred at (gu) : 90.49390 88.91723 87.44447 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71119 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17324 grid for indexing accessible points = 1.400000 m= 28607 mr = 50597 m= 5423 mr = 21815 m= 450 mr = 3606 m= 7 mr = 214 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 29374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15506 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) : 0.6866357 object centre at (A) : 41.46650 15.08100 45.94750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7366809E-02 3.6987431E-02 midg,1,midg; midg,igrid,midg 2.2369578E-02 9.5297946E-03 1,midg,midg; igrid,midg,midg 3.0399818E-02 1.1052443E-02 gauss-seidel spectral radius is 0.9987673 estimated iterations to convergence 226 setup time was (sec) 0.5800000 now iterating at: 05:29:53 rms-change max change #iterations 4.355120 176.6647 at 10iterations 2.125314 71.53937 at 20iterations 1.033982 42.39599 at 30iterations 0.5074018 17.85988 at 40iterations 0.2471589 9.398693 at 50iterations 0.1204340 3.588791 at 60iterations 5.8738429E-02 1.735283 at 70iterations 2.8639318E-02 0.9179177 at 80iterations 1.4027993E-02 0.4277697 at 90iterations 6.8731317E-03 0.2203417 at 100iterations 3.3735894E-03 9.9506378E-02 at 110iterations 1.6877255E-03 5.8345318E-02 at 120iterations finished qdiffx linear iterations at : 05:30:00 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 1.6877255E-03 5.8345318E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 05:30:02 7.850u 0.215s 0:09.05 89.0% 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 05:30:02 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2277 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: 3.089860 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): 19.77000 63.16300 ymin,ymax (A): -3.556000 33.71800 zmin,zma (A): 20.02400 71.87100 x,y,z range (A): 43.39300 37.27400 51.84700 scale (grids/A): 3.089860 object centre (A): 41.46650 15.08100 45.94750 number of atom coordinates read : 2277 total number of charged atoms : 1957 net assigned charge : 6.500009 assigned positive charge : 316.7440 centred at (gu) : 90.13020 88.23943 86.38760 assigned negative charge : -310.2442 centred at (gu) : 90.74091 88.37592 86.16682 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 163996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17324 grid for indexing accessible points = 1.400000 m= 89509 mr = 121727 m= 36050 mr = 74729 m= 10261 mr = 29772 m= 1893 mr = 7948 m= 193 mr = 1389 m= 5 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 66218 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 15655 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) : 2.059907 object centre at (A) : 41.46650 15.08100 45.94750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4394985 0.2972353 midg,1,midg; midg,igrid,midg 0.1993134 8.1354618E-02 1,midg,midg; igrid,midg,midg 0.2728711 0.2482798 gauss-seidel spectral radius is 0.9992785 estimated iterations to convergence 294 setup time was (sec) 1.320000 now iterating at: 05:30:03 rms-change max change #iterations 9.858710 345.9091 at 10iterations 5.823059 135.7362 at 20iterations 3.426537 73.68379 at 30iterations 2.007715 43.11097 at 40iterations 1.174051 28.18836 at 50iterations 0.6863003 14.72199 at 60iterations 0.4007038 7.279284 at 70iterations 0.2331533 5.166862 at 80iterations 0.1360138 2.428028 at 90iterations 7.9253651E-02 1.408527 at 100iterations 4.6170514E-02 0.8793612 at 110iterations 2.6861541E-02 0.5423012 at 120iterations 1.5713496E-02 0.2751465 at 130iterations 9.1939354E-03 0.1727905 at 140iterations 5.4350337E-03 0.1011887 at 150iterations 3.2607091E-03 5.5582047E-02 at 160iterations 2.0299200E-03 3.6827087E-02 at 170iterations 1.3169320E-03 2.4368286E-02 at 180iterations finished qdiffx linear iterations at : 05:30:14 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 1.3169320E-03 2.4368286E-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) 12.59000 DelPhi exited at 05:30:15 12.595u 0.211s 0:13.72 93.2% 0+0k 0+0io 0pf+0w