Sun Oct 9 11:13:33 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 Sun Oct 9 2011 at 11:13:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 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: 0.6382216 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): -25.68900 24.82700 ymin,ymax (A): -30.62000 25.16000 zmin,zma (A): -1.897000 45.30500 x,y,z range (A): 50.51600 55.78000 47.20200 scale (grids/A): 0.6382216 object centre (A): -0.4310007 -2.730000 21.70400 number of atom coordinates read : 2392 total number of charged atoms : 2269 net assigned charge : -1.499981 assigned positive charge : 346.2990 centred at (gu) : 91.33179 92.15993 89.14548 assigned negative charge : -347.8000 centred at (gu) : 91.28890 92.22536 89.35365 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6873 nv = 96 ne = 84 npr = 46902 no. pairs analyzed = 46902 no. exposed pairs = 3499 no. arc points = 24566 no. surface atoms = 1172 nbur = 1220 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 387 mr = 3391 m= 0 mr = 41 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3828 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2242 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7976 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1705155E-08 -1.9258810E-08 midg,1,midg; midg,igrid,midg 2.6536497E-09 -1.3877516E-08 1,midg,midg; igrid,midg,midg -4.8124162E-09 2.8347111E-09 gauss-seidel spectral radius is 0.9872789 estimated iterations to convergence 72 setup time was (sec) 0.5000000 now iterating at: 11:13:34 rms-change max change #iterations 0.1338753 19.84766 at 10iterations 1.3040547E-02 2.118477 at 20iterations 1.3061793E-03 0.1845064 at 30iterations 1.3502476E-04 2.5218487E-02 at 40iterations 1.8575063E-05 3.6535263E-03 at 50iterations finished qdiffx linear iterations at : 11:13:37 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.8575063E-05 3.6535263E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 11:13:37 3.328u 0.195s 0:03.89 90.2% 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 Sun Oct 9 2011 at 11:13:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 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: 1.914665 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): -25.68900 24.82700 ymin,ymax (A): -30.62000 25.16000 zmin,zma (A): -1.897000 45.30500 x,y,z range (A): 50.51600 55.78000 47.20200 scale (grids/A): 1.914665 object centre (A): -0.4310007 -2.730000 21.70400 number of atom coordinates read : 2392 total number of charged atoms : 2269 net assigned charge : -1.499981 assigned positive charge : 346.2990 centred at (gu) : 93.99499 96.47910 87.43577 assigned negative charge : -347.8000 centred at (gu) : 93.86674 96.67621 88.06097 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 73178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24566 grid for indexing accessible points = 1.400000 m= 25946 mr = 47966 m= 4488 mr = 18067 m= 280 mr = 2598 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 491 time to turn everything in is 0.5200000 number of dielectric boundary points 35181 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 17863 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) : 0.6382216 object centre at (A) : -0.4310007 -2.730000 21.70400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1276290E-02 -1.8774621E-02 midg,1,midg; midg,igrid,midg 2.7155583E-03 -2.3742501E-02 1,midg,midg; igrid,midg,midg -9.0314373E-03 1.0485523E-02 gauss-seidel spectral radius is 0.9986498 estimated iterations to convergence 216 setup time was (sec) 0.8200000 now iterating at: 11:13:38 rms-change max change #iterations 4.032250 156.2685 at 10iterations 1.883053 67.93119 at 20iterations 0.8860050 32.87682 at 30iterations 0.4146747 12.31604 at 40iterations 0.1948222 7.001321 at 50iterations 9.1213994E-02 2.812088 at 60iterations 4.2902965E-02 1.360464 at 70iterations 2.0151323E-02 0.6462784 at 80iterations 9.4892327E-03 0.2944450 at 90iterations 4.4511301E-03 0.1421776 at 100iterations 2.0940762E-03 6.7478180E-02 at 110iterations 9.8429597E-04 3.2161713E-02 at 120iterations finished qdiffx linear iterations at : 11:13:45 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 9.8429597E-04 3.2161713E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 11:13:46 7.654u 0.244s 0:08.32 94.8% 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 Sun Oct 9 2011 at 11:13:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 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: 2.871997 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): -25.68900 24.82700 ymin,ymax (A): -30.62000 25.16000 zmin,zma (A): -1.897000 45.30500 x,y,z range (A): 50.51600 55.78000 47.20200 scale (grids/A): 2.871997 object centre (A): -0.4310007 -2.730000 21.70400 number of atom coordinates read : 2392 total number of charged atoms : 2269 net assigned charge : -1.499981 assigned positive charge : 346.2990 centred at (gu) : 95.99222 99.71848 86.15364 assigned negative charge : -347.8000 centred at (gu) : 95.79999 100.0142 87.09132 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 168876 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24566 grid for indexing accessible points = 1.400000 m= 82636 mr = 117386 m= 31237 mr = 64903 m= 8052 mr = 24039 m= 1204 mr = 5675 m= 57 mr = 744 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 1707 time to turn everything in is 1.330000 number of dielectric boundary points 79305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 18150 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) : 1.914665 object centre at (A) : -0.4310007 -2.730000 21.70400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2039799 -0.1652211 midg,1,midg; midg,igrid,midg 5.8079883E-02 -0.2099577 1,midg,midg; igrid,midg,midg -0.1743283 0.1092319 gauss-seidel spectral radius is 0.9992716 estimated iterations to convergence 292 setup time was (sec) 1.670000 now iterating at: 11:13:48 rms-change max change #iterations 9.651970 351.7675 at 10iterations 5.724647 135.4150 at 20iterations 3.385574 76.81059 at 30iterations 1.994784 44.08543 at 40iterations 1.170300 21.71296 at 50iterations 0.6814379 13.80447 at 60iterations 0.3975071 7.434975 at 70iterations 0.2309365 4.511166 at 80iterations 0.1340317 2.567955 at 90iterations 7.7701084E-02 1.415810 at 100iterations 4.5116264E-02 0.8513536 at 110iterations 2.6078608E-02 0.5140285 at 120iterations 1.5107829E-02 0.2564621 at 130iterations 8.7326206E-03 0.1644020 at 140iterations 5.0445730E-03 9.2707157E-02 at 150iterations 2.9160583E-03 5.1743507E-02 at 160iterations 1.6864204E-03 3.3361435E-02 at 170iterations 9.7503536E-04 1.9744873E-02 at 180iterations finished qdiffx linear iterations at : 11:13:58 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 9.7503536E-04 1.9744873E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 11:13:59 12.577u 0.226s 0:13.19 96.9% 0+0k 0+0io 0pf+0w