Tue Oct 11 08:01:55 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 08:01:56 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2825 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6194213 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): -22.07000 29.04900 ymin,ymax (A): 12.28100 63.85600 zmin,zma (A): -9.915999 47.55700 x,y,z range (A): 51.11900 51.57500 57.47300 scale (grids/A): 0.6194213 object centre (A): 3.489500 38.06850 18.82050 number of atom coordinates read : 2825 total number of charged atoms : 2656 net assigned charge : 7.000020 assigned positive charge : 418.0794 centred at (gu) : 90.58002 89.66180 91.34400 assigned negative charge : -411.0804 centred at (gu) : 90.67113 89.64830 91.51872 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7275 nv = 96 ne = 84 npr = 56101 no. pairs analyzed = 56101 no. exposed pairs = 3777 no. arc points = 26597 no. surface atoms = 1275 nbur = 1550 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 333 mr = 3709 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3300000 number of dielectric boundary points 3879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2625 ## 260 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8850 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3106937E-08 -8.9907246E-09 midg,1,midg; midg,igrid,midg 5.1907749E-09 6.2280758E-09 1,midg,midg; igrid,midg,midg 1.0564336E-08 -7.1478456E-10 gauss-seidel spectral radius is 0.9865314 estimated iterations to convergence 71 setup time was (sec) 0.5700000 now iterating at: 08:01:56 rms-change max change #iterations 0.1296711 19.74872 at 10iterations 1.1637025E-02 1.658308 at 20iterations 1.0761986E-03 0.1576748 at 30iterations 9.9672448E-05 1.4953613E-02 at 40iterations 9.3972703E-06 1.2240410E-03 at 50iterations finished qdiffx linear iterations at : 08:01:59 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 9.3972703E-06 1.2240410E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 08:02:00 3.551u 0.201s 0:04.05 92.5% 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 08:02:00 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2825 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: 1.858264 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): -22.07000 29.04900 ymin,ymax (A): 12.28100 63.85600 zmin,zma (A): -9.915999 47.55700 x,y,z range (A): 51.11900 51.57500 57.47300 scale (grids/A): 1.858264 object centre (A): 3.489500 38.06850 18.82050 number of atom coordinates read : 2825 total number of charged atoms : 2656 net assigned charge : 7.000020 assigned positive charge : 418.0794 centred at (gu) : 91.73928 88.98502 94.03130 assigned negative charge : -411.0804 centred at (gu) : 92.01332 88.94470 94.55621 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 78648 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26597 grid for indexing accessible points = 1.400000 m= 25305 mr = 52408 m= 3277 mr = 17492 m= 163 mr = 1731 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 35727 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 197 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20830 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) : 0.6194213 object centre at (A) : 3.489500 38.06850 18.82050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8509859E-02 5.7835355E-03 midg,1,midg; midg,igrid,midg 4.1162646E-03 1.0662930E-02 1,midg,midg; igrid,midg,midg -1.9478668E-03 -7.2946637E-03 gauss-seidel spectral radius is 0.9985995 estimated iterations to convergence 212 setup time was (sec) 0.9200000 now iterating at: 08:02:01 rms-change max change #iterations 4.190523 157.7018 at 10iterations 1.932765 65.13685 at 20iterations 0.8912375 28.20278 at 30iterations 0.4124334 12.73392 at 40iterations 0.1917952 6.206810 at 50iterations 8.8566825E-02 2.939949 at 60iterations 4.0915534E-02 1.213249 at 70iterations 1.8946240E-02 0.6371632 at 80iterations 8.7924758E-03 0.2917967 at 90iterations 4.0753740E-03 0.1300583 at 100iterations 1.8836738E-03 5.6234360E-02 at 110iterations 8.7431452E-04 2.7544022E-02 at 120iterations finished qdiffx linear iterations at : 08:02:08 total time elapsed so far: 8.140000 # loops : 120 mean,max change (kT/e) : 8.7431452E-04 2.7544022E-02 energy calculations done at 8.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.320000 DelPhi exited at 08:02:09 8.325u 0.235s 0:08.99 95.1% 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 08:02:09 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2825 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.787396 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): -22.07000 29.04900 ymin,ymax (A): 12.28100 63.85600 zmin,zma (A): -9.915999 47.55700 x,y,z range (A): 51.11900 51.57500 57.47300 scale (grids/A): 2.787396 object centre (A): 3.489500 38.06850 18.82050 number of atom coordinates read : 2825 total number of charged atoms : 2656 net assigned charge : 7.000020 assigned positive charge : 418.0794 centred at (gu) : 92.60870 88.47733 96.04667 assigned negative charge : -411.0804 centred at (gu) : 93.01994 88.41693 96.83432 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 182231 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26597 grid for indexing accessible points = 1.400000 m= 84589 mr = 127833 m= 26927 mr = 66890 m= 5514 mr = 20464 m= 639 mr = 3668 m= 29 mr = 317 m= 0 mr = 0 time to grow re-entrant surface = 0.8299999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.460000 number of dielectric boundary points 80757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 21245 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) : 1.858264 object centre at (A) : 3.489500 38.06850 18.82050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5681508 0.1469834 midg,1,midg; midg,igrid,midg 5.5470407E-02 0.1806012 1,midg,midg; igrid,midg,midg 1.0921959E-02 9.8522818E-03 gauss-seidel spectral radius is 0.9992646 estimated iterations to convergence 291 setup time was (sec) 1.780000 now iterating at: 08:02:11 rms-change max change #iterations 10.01762 345.9706 at 10iterations 5.909357 167.2719 at 20iterations 3.444770 68.22211 at 30iterations 2.003932 40.83483 at 40iterations 1.159374 20.95673 at 50iterations 0.6714718 13.24759 at 60iterations 0.3872949 7.727801 at 70iterations 0.2239197 4.548828 at 80iterations 0.1289258 2.799234 at 90iterations 7.4252822E-02 1.364820 at 100iterations 4.2786259E-02 0.7492466 at 110iterations 2.4557911E-02 0.4484487 at 120iterations 1.4158808E-02 0.2677155 at 130iterations 8.1459368E-03 0.1567184 at 140iterations 4.6768403E-03 8.6715698E-02 at 150iterations 2.6954161E-03 4.9357176E-02 at 160iterations 1.5463523E-03 2.9760361E-02 at 170iterations 8.9125941E-04 1.8253326E-02 at 180iterations finished qdiffx linear iterations at : 08:02:22 total time elapsed so far: 13.56000 # loops : 180 mean,max change (kT/e) : 8.9125941E-04 1.8253326E-02 energy calculations done at 13.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.76000 DelPhi exited at 08:02:23 13.758u 0.241s 0:14.32 97.6% 0+0k 0+0io 0pf+0w