Sat Oct 8 20:25:06 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 Sat Oct 8 2011 at 20:25:06 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6340386 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): -10.95400 38.80900 ymin,ymax (A): -21.95500 24.32800 zmin,zma (A): -12.40700 43.74100 x,y,z range (A): 49.76300 46.28300 56.14800 scale (grids/A): 0.6340386 object centre (A): 13.92750 1.186500 15.66700 number of atom coordinates read : 2581 total number of charged atoms : 2461 net assigned charge : 3.948002 assigned positive charge : 395.3610 centred at (gu) : 88.69576 89.31018 89.97187 assigned negative charge : -391.4136 centred at (gu) : 88.60116 89.34970 89.86945 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6816 nv = 96 ne = 84 npr = 53700 no. pairs analyzed = 53700 no. exposed pairs = 2979 no. arc points = 21632 no. surface atoms = 995 nbur = 1586 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 366 mr = 3851 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 164 time to turn everything in is 0.1900000 number of dielectric boundary points 3296 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2110 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8342 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4087250E-09 1.4947966E-08 midg,1,midg; midg,igrid,midg 1.0283232E-08 8.8743141E-10 1,midg,midg; igrid,midg,midg -6.2167431E-09 1.0794793E-08 gauss-seidel spectral radius is 0.9871082 estimated iterations to convergence 72 setup time was (sec) 0.4100000 now iterating at: 20:25:06 rms-change max change #iterations 0.1439175 22.65818 at 10iterations 1.3789093E-02 2.123194 at 20iterations 1.3597715E-03 0.2144647 at 30iterations 1.3041077E-04 1.7576218E-02 at 40iterations 1.2819153E-05 1.8291473E-03 at 50iterations finished qdiffx linear iterations at : 20:25:09 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 1.2819153E-05 1.8291473E-03 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 20:25:10 3.687u 0.207s 0:04.17 93.0% 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 Sat Oct 8 2011 at 20:25:10 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.902116 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): -10.95400 38.80900 ymin,ymax (A): -21.95500 24.32800 zmin,zma (A): -12.40700 43.74100 x,y,z range (A): 49.76300 46.28300 56.14800 scale (grids/A): 1.902116 object centre (A): 13.92750 1.186500 15.66700 number of atom coordinates read : 2581 total number of charged atoms : 2461 net assigned charge : 3.948002 assigned positive charge : 395.3610 centred at (gu) : 86.08674 87.93001 89.91527 assigned negative charge : -391.4136 centred at (gu) : 85.80318 88.04891 89.60825 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21632 grid for indexing accessible points = 1.400000 m= 25962 mr = 51800 m= 3816 mr = 19377 m= 223 mr = 2380 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 4468 time to turn everything in is 0.3700000 number of dielectric boundary points 30243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 19354 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) : 0.6340386 object centre at (A) : 13.92750 1.186500 15.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9551188E-02 2.3939537E-02 midg,1,midg; midg,igrid,midg 1.2579811E-02 1.4318125E-03 1,midg,midg; igrid,midg,midg -1.9154354E-03 3.8961411E-02 gauss-seidel spectral radius is 0.9986279 estimated iterations to convergence 214 setup time was (sec) 0.6100000 now iterating at: 20:25:11 rms-change max change #iterations 4.260503 173.2035 at 10iterations 1.994596 66.89784 at 20iterations 0.9334804 32.49689 at 30iterations 0.4353520 12.98029 at 40iterations 0.2037798 6.799008 at 50iterations 9.5345087E-02 3.544559 at 60iterations 4.4687826E-02 1.452195 at 70iterations 2.0895598E-02 0.6317616 at 80iterations 9.7793518E-03 0.3483216 at 90iterations 4.5543364E-03 0.1388741 at 100iterations 2.1397618E-03 6.2576294E-02 at 110iterations 1.0029151E-03 3.3605576E-02 at 120iterations finished qdiffx linear iterations at : 20:25:18 total time elapsed so far: 8.390000 # loops : 120 mean,max change (kT/e) : 1.0029151E-03 3.3605576E-02 energy calculations done at 8.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.520000 DelPhi exited at 20:25:19 8.526u 0.254s 0:09.04 97.0% 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 Sat Oct 8 2011 at 20:25:19 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.853174 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): -10.95400 38.80900 ymin,ymax (A): -21.95500 24.32800 zmin,zma (A): -12.40700 43.74100 x,y,z range (A): 49.76300 46.28300 56.14800 scale (grids/A): 2.853174 object centre (A): 13.92750 1.186500 15.66700 number of atom coordinates read : 2581 total number of charged atoms : 2461 net assigned charge : 3.948002 assigned positive charge : 395.3610 centred at (gu) : 84.12991 86.89508 89.87261 assigned negative charge : -391.4136 centred at (gu) : 83.70469 87.07350 89.41226 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 170913 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21632 grid for indexing accessible points = 1.400000 m= 85203 mr = 125157 m= 29403 mr = 70444 m= 6831 mr = 23760 m= 812 mr = 5124 m= 38 mr = 519 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 15274 time to turn everything in is 0.9700000 number of dielectric boundary points 68183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 19688 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) : 1.902116 object centre at (A) : 13.92750 1.186500 15.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1338686 0.2817043 midg,1,midg; midg,igrid,midg 0.1443200 2.2396671E-02 1,midg,midg; igrid,midg,midg -1.1473983E-03 0.4664935 gauss-seidel spectral radius is 0.9992502 estimated iterations to convergence 288 setup time was (sec) 1.230000 now iterating at: 20:25:20 rms-change max change #iterations 9.816743 343.3911 at 10iterations 5.665041 146.6655 at 20iterations 3.247619 65.95592 at 30iterations 1.857549 37.27506 at 40iterations 1.064879 19.65055 at 50iterations 0.6082539 11.93398 at 60iterations 0.3486036 6.587502 at 70iterations 0.1995775 3.592920 at 80iterations 0.1142269 2.003798 at 90iterations 6.5368794E-02 1.239281 at 100iterations 3.7308075E-02 0.7375269 at 110iterations 2.1350777E-02 0.3880424 at 120iterations 1.2200552E-02 0.2271261 at 130iterations 7.0027979E-03 0.1399803 at 140iterations 4.0032566E-03 7.1327209E-02 at 150iterations 2.2878528E-03 4.0925980E-02 at 160iterations 1.3067516E-03 2.4642944E-02 at 170iterations 7.4803724E-04 1.4228821E-02 at 180iterations finished qdiffx linear iterations at : 20:25:33 total time elapsed so far: 13.65000 # loops : 180 mean,max change (kT/e) : 7.4803724E-04 1.4228821E-02 energy calculations done at 13.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.79000 DelPhi exited at 20:25:33 13.787u 0.265s 0:14.32 98.0% 0+0k 0+0io 0pf+0w