Wed Feb 15 08:55:12 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:12 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 = 2356 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: 0.6717362 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): -3.322000 49.67500 ymin,ymax (A): 41.91600 88.64900 zmin,zma (A): -4.612000 41.60900 x,y,z range (A): 52.99700 46.73300 46.22100 scale (grids/A): 0.6717362 object centre (A): 23.17650 65.28250 18.49850 number of atom coordinates read : 2356 total number of charged atoms : 2219 net assigned charge : -0.9999951 assigned positive charge : 339.5872 centred at (gu) : 90.63971 90.86087 89.88457 assigned negative charge : -340.5879 centred at (gu) : 90.53927 90.97269 89.94965 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7122 nv = 96 ne = 84 npr = 50574 no. pairs analyzed = 50574 no. exposed pairs = 2873 no. arc points = 20280 no. surface atoms = 979 nbur = 1377 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 450 mr = 3941 m= 4 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1899 ## 138 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8364 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1986646E-08 -1.8210363E-08 midg,1,midg; midg,igrid,midg 1.8694367E-08 -3.5614523E-08 1,midg,midg; igrid,midg,midg -2.3685855E-08 2.2673268E-08 gauss-seidel spectral radius is 0.9884890 estimated iterations to convergence 76 setup time was (sec) 0.5400000 now iterating at: 08:55:13 rms-change max change #iterations 0.1643942 24.01219 at 10iterations 1.8223412E-02 2.449104 at 20iterations 1.9915937E-03 0.2819262 at 30iterations 2.2262789E-04 3.2485962E-02 at 40iterations 2.5217407E-05 4.1475296E-03 at 50iterations finished qdiffx linear iterations at : 08:55:15 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 2.5217407E-05 4.1475296E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 08:55:16 3.418u 0.161s 0:04.27 83.6% 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 Wed Feb 15 2012 at 08:55:16 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 = 2356 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.015208 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): -3.322000 49.67500 ymin,ymax (A): 41.91600 88.64900 zmin,zma (A): -4.612000 41.60900 x,y,z range (A): 52.99700 46.73300 46.22100 scale (grids/A): 2.015208 object centre (A): 23.17650 65.28250 18.49850 number of atom coordinates read : 2356 total number of charged atoms : 2219 net assigned charge : -0.9999951 assigned positive charge : 339.5872 centred at (gu) : 91.91868 92.58212 89.65323 assigned negative charge : -340.5879 centred at (gu) : 91.61774 92.91809 89.84888 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 75959 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20280 grid for indexing accessible points = 1.400000 m= 28167 mr = 52810 m= 5169 mr = 20858 m= 416 mr = 3297 m= 12 mr = 202 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1127 time to turn everything in is 0.6000000 number of dielectric boundary points 32556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 17596 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) : 0.6717362 object centre at (A) : 23.17650 65.28250 18.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2084442E-04 -3.6429614E-02 midg,1,midg; midg,igrid,midg 1.8771868E-02 -4.2830490E-02 1,midg,midg; igrid,midg,midg 7.9169981E-03 6.7171015E-02 gauss-seidel spectral radius is 0.9987507 estimated iterations to convergence 224 setup time was (sec) 0.9100000 now iterating at: 08:55:17 rms-change max change #iterations 4.366641 208.6966 at 10iterations 2.111907 75.84424 at 20iterations 1.025011 30.68568 at 30iterations 0.4939747 16.11728 at 40iterations 0.2393027 6.928671 at 50iterations 0.1160109 4.342659 at 60iterations 5.6092873E-02 1.674633 at 70iterations 2.7112367E-02 0.8376942 at 80iterations 1.3173007E-02 0.4298630 at 90iterations 6.3488130E-03 0.1929359 at 100iterations 3.0881474E-03 9.3467712E-02 at 110iterations 1.4958272E-03 4.6321869E-02 at 120iterations finished qdiffx linear iterations at : 08:55:24 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 1.4958272E-03 4.6321869E-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) 7.680000 DelPhi exited at 08:55:24 7.683u 0.206s 0:08.23 95.7% 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 Wed Feb 15 2012 at 08:55:25 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 = 2356 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.022813 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): -3.322000 49.67500 ymin,ymax (A): 41.91600 88.64900 zmin,zma (A): -4.612000 41.60900 x,y,z range (A): 52.99700 46.73300 46.22100 scale (grids/A): 3.022813 object centre (A): 23.17650 65.28250 18.49850 number of atom coordinates read : 2356 total number of charged atoms : 2219 net assigned charge : -0.9999951 assigned positive charge : 339.5872 centred at (gu) : 92.87804 93.87317 89.47974 assigned negative charge : -340.5879 centred at (gu) : 92.42662 94.37716 89.77323 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 175713 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20280 grid for indexing accessible points = 1.400000 m= 89063 mr = 128091 m= 35064 mr = 72950 m= 9535 mr = 28309 m= 1685 mr = 7261 m= 177 mr = 1160 m= 5 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 3979 time to turn everything in is 1.500000 number of dielectric boundary points 73355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 17752 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) : 2.015208 object centre at (A) : 23.17650 65.28250 18.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4991181E-02 -0.2802222 midg,1,midg; midg,igrid,midg 0.2948105 -0.4292524 1,midg,midg; igrid,midg,midg 0.1545858 0.6826445 gauss-seidel spectral radius is 0.9992819 estimated iterations to convergence 294 setup time was (sec) 1.800000 now iterating at: 08:55:27 rms-change max change #iterations 10.04148 406.7831 at 10iterations 5.883554 117.8606 at 20iterations 3.448546 67.68962 at 30iterations 2.010294 39.32146 at 40iterations 1.174423 22.62786 at 50iterations 0.6843053 11.36812 at 60iterations 0.3986173 7.773479 at 70iterations 0.2318308 5.577875 at 80iterations 0.1348411 2.571047 at 90iterations 7.8275084E-02 1.372666 at 100iterations 4.5378327E-02 0.7540207 at 110iterations 2.6396036E-02 0.4729112 at 120iterations 1.5314472E-02 0.2525215 at 130iterations 8.8789221E-03 0.1622505 at 140iterations 5.1475083E-03 8.9651585E-02 at 150iterations 2.9840101E-03 5.1715851E-02 at 160iterations 1.7298801E-03 2.9552460E-02 at 170iterations 1.0042330E-03 1.8142700E-02 at 180iterations finished qdiffx linear iterations at : 08:55:38 total time elapsed so far: 13.09000 # loops : 180 mean,max change (kT/e) : 1.0042330E-03 1.8142700E-02 energy calculations done at 13.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.28000 DelPhi exited at 08:55:38 13.286u 0.236s 0:13.92 97.0% 0+0k 0+0io 0pf+0w