Sat Oct 15 15:22:50 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 15 2011 at 15:22:50 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2724 !!! WARNING: HIR 43 has a net charge of 0.5140 !!! WARNING: TRP 148 has a net charge of -0.2720 !!! WARNING: ASP 292 has a net charge of -0.2720 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: 0.6664919 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): -7.696000 40.31900 ymin,ymax (A): -26.17900 21.59200 zmin,zma (A): -9.874000 43.54000 x,y,z range (A): 48.01500 47.77100 53.41400 scale (grids/A): 0.6664919 object centre (A): 16.31150 -2.293500 16.83300 number of atom coordinates read : 2724 total number of charged atoms : 2576 net assigned charge : 1.970018 assigned positive charge : 415.5436 centred at (gu) : 89.69714 90.20434 88.76669 assigned negative charge : -413.5743 centred at (gu) : 89.92545 90.04382 88.82983 start vw surface at 0.1200000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8027 nv = 96 ne = 84 npr = 55513 no. pairs analyzed = 55513 no. exposed pairs = 3311 no. arc points = 22808 no. surface atoms = 1125 nbur = 1599 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 477 mr = 4539 m= 2 mr = 64 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 0.3300000 number of dielectric boundary points 3903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2259 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9513 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7347328E-08 -7.8324547E-09 midg,1,midg; midg,igrid,midg -3.3501045E-08 4.6717858E-08 1,midg,midg; igrid,midg,midg 6.4919135E-08 -4.9266035E-08 gauss-seidel spectral radius is 0.9883392 estimated iterations to convergence 76 setup time was (sec) 0.6500000 now iterating at: 15:22:51 rms-change max change #iterations 0.1830342 26.99838 at 10iterations 2.0373687E-02 2.758480 at 20iterations 2.3437554E-03 0.2975464 at 30iterations 3.2160565E-04 4.1534424E-02 at 40iterations 6.8866837E-05 9.2620850E-03 at 50iterations finished qdiffx linear iterations at : 15:22:58 total time elapsed so far: 5.270000 # loops : 50 mean,max change (kT/e) : 6.8866837E-05 9.2620850E-03 energy calculations done at 5.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.440000 DelPhi exited at 15:22:58 5.447u 0.450s 0:08.11 72.6% 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 Sat Oct 15 2011 at 15:22:58 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2724 !!! WARNING: HIR 43 has a net charge of 0.5140 !!! WARNING: TRP 148 has a net charge of -0.2720 !!! WARNING: ASP 292 has a net charge of -0.2720 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: 1.999476 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): -7.696000 40.31900 ymin,ymax (A): -26.17900 21.59200 zmin,zma (A): -9.874000 43.54000 x,y,z range (A): 48.01500 47.77100 53.41400 scale (grids/A): 1.999476 object centre (A): 16.31150 -2.293500 16.83300 number of atom coordinates read : 2724 total number of charged atoms : 2576 net assigned charge : 1.970018 assigned positive charge : 415.5436 centred at (gu) : 89.09075 90.61244 86.29946 assigned negative charge : -413.5743 centred at (gu) : 89.77606 90.13117 86.48911 start vw surface at 0.1200000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 85576 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22808 grid for indexing accessible points = 1.400000 m= 33098 mr = 60110 m= 6046 mr = 24873 m= 407 mr = 4001 m= 7 mr = 157 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 35993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 20382 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) : 0.6664919 object centre at (A) : 16.31150 -2.293500 16.83300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1992342E-03 -5.2951746E-02 midg,1,midg; midg,igrid,midg -2.1771405E-02 3.1044176E-02 1,midg,midg; igrid,midg,midg 8.3027683E-02 -7.9002194E-03 gauss-seidel spectral radius is 0.9987679 estimated iterations to convergence 226 setup time was (sec) 1.100000 now iterating at: 15:23:01 rms-change max change #iterations 4.861941 226.7115 at 10iterations 2.375413 99.00609 at 20iterations 1.161297 35.07976 at 30iterations 0.5667858 16.60721 at 40iterations 0.2762212 9.090670 at 50iterations 0.1349568 3.750893 at 60iterations 6.6054858E-02 1.977470 at 70iterations 3.2288238E-02 0.9303398 at 80iterations 1.5847867E-02 0.4776068 at 90iterations 7.8361034E-03 0.2421331 at 100iterations 3.9510061E-03 0.1140137 at 110iterations 2.0568466E-03 6.2829971E-02 at 120iterations finished qdiffx linear iterations at : 15:23:20 total time elapsed so far: 13.99000 # loops : 120 mean,max change (kT/e) : 2.0568466E-03 6.2829971E-02 energy calculations done at 13.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.15000 DelPhi exited at 15:23:20 14.157u 0.554s 0:22.24 66.0% 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 15 2011 at 15:23:20 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2724 !!! WARNING: HIR 43 has a net charge of 0.5140 !!! WARNING: TRP 148 has a net charge of -0.2720 !!! WARNING: ASP 292 has a net charge of -0.2720 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: 2.999214 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): -7.696000 40.31900 ymin,ymax (A): -26.17900 21.59200 zmin,zma (A): -9.874000 43.54000 x,y,z range (A): 48.01500 47.77100 53.41400 scale (grids/A): 2.999214 object centre (A): 16.31150 -2.293500 16.83300 number of atom coordinates read : 2724 total number of charged atoms : 2576 net assigned charge : 1.970018 assigned positive charge : 415.5436 centred at (gu) : 88.63600 90.91848 84.44907 assigned negative charge : -413.5743 centred at (gu) : 89.66399 90.19663 84.73359 start vw surface at 0.1100000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 197662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22808 grid for indexing accessible points = 1.400000 m= 104550 mr = 145386 m= 41516 mr = 86313 m= 11200 mr = 33972 m= 1831 mr = 8679 m= 167 mr = 1225 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.970000 number of dielectric boundary points 81281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 20606 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) : 1.999476 object centre at (A) : 16.31150 -2.293500 16.83300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1201235 -0.6648098 midg,1,midg; midg,igrid,midg -0.2241302 0.3908500 1,midg,midg; igrid,midg,midg 0.6900568 -3.0058978E-02 gauss-seidel spectral radius is 0.9992915 estimated iterations to convergence 296 setup time was (sec) 2.370000 now iterating at: 15:23:24 rms-change max change #iterations 11.15770 440.5924 at 10iterations 6.604947 139.2717 at 20iterations 3.882968 72.53819 at 30iterations 2.292381 45.72424 at 40iterations 1.344598 24.83257 at 50iterations 0.7900888 13.92244 at 60iterations 0.4615242 8.366142 at 70iterations 0.2706901 4.987328 at 80iterations 0.1584419 2.557259 at 90iterations 9.2710525E-02 1.564804 at 100iterations 5.4224201E-02 0.8697090 at 110iterations 3.1818185E-02 0.5352516 at 120iterations 1.8754877E-02 0.3100372 at 130iterations 1.1153599E-02 0.2181501 at 140iterations 6.7506791E-03 0.1383400 at 150iterations 4.2120316E-03 9.2315674E-02 at 160iterations 2.7492517E-03 5.8935165E-02 at 170iterations 1.9037059E-03 4.4525146E-02 at 180iterations finished qdiffx linear iterations at : 15:23:54 total time elapsed so far: 23.05000 # loops : 180 mean,max change (kT/e) : 1.9037059E-03 4.4525146E-02 energy calculations done at 23.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.22000 DelPhi exited at 15:23:55 23.225u 0.618s 0:35.04 68.0% 0+0k 0+0io 0pf+0w