Tue Oct 11 00:32:25 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 Tue Oct 11 2011 at 00:32:25 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 = 2620 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: 0.6272575 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): 9.811001 59.65800 ymin,ymax (A): -0.2340000 56.52100 zmin,zma (A): 9.641000 52.44300 x,y,z range (A): 49.84700 56.75500 42.80200 scale (grids/A): 0.6272575 object centre (A): 34.73450 28.14350 31.04200 number of atom coordinates read : 2620 total number of charged atoms : 2479 net assigned charge : 8.000013 assigned positive charge : 395.0007 centred at (gu) : 89.87428 90.96678 89.97119 assigned negative charge : -387.0014 centred at (gu) : 89.89293 90.76546 90.09854 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6768 nv = 96 ne = 84 npr = 53311 no. pairs analyzed = 53311 no. exposed pairs = 3082 no. arc points = 21429 no. surface atoms = 1037 nbur = 1583 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 360 mr = 3857 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.3500000 number of dielectric boundary points 3229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2074 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8264 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8219536E-08 -2.6683711E-09 midg,1,midg; midg,igrid,midg -7.1524999E-09 2.9583841E-08 1,midg,midg; igrid,midg,midg 9.6285131E-09 6.1680527E-09 gauss-seidel spectral radius is 0.9868326 estimated iterations to convergence 71 setup time was (sec) 0.6700000 now iterating at: 00:32:26 rms-change max change #iterations 0.1330856 21.13103 at 10iterations 1.3139759E-02 2.798309 at 20iterations 1.6464664E-03 0.3048401 at 30iterations 3.3866099E-04 7.4954987E-02 at 40iterations 8.4730076E-05 1.9947052E-02 at 50iterations finished qdiffx linear iterations at : 00:32:29 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 8.4730076E-05 1.9947052E-02 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 00:32:30 4.240u 0.227s 0:04.87 91.5% 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 00:32:30 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 = 2620 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: 1.881773 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): 9.811001 59.65800 ymin,ymax (A): -0.2340000 56.52100 zmin,zma (A): 9.641000 52.44300 x,y,z range (A): 49.84700 56.75500 42.80200 scale (grids/A): 1.881773 object centre (A): 34.73450 28.14350 31.04200 number of atom coordinates read : 2620 total number of charged atoms : 2479 net assigned charge : 8.000013 assigned positive charge : 395.0007 centred at (gu) : 89.62218 92.89992 89.91281 assigned negative charge : -387.0014 centred at (gu) : 89.67854 92.29604 90.29544 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 73625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21429 grid for indexing accessible points = 1.400000 m= 26860 mr = 52028 m= 4188 mr = 20332 m= 200 mr = 2744 m= 3 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 2059 time to turn everything in is 0.6300000 number of dielectric boundary points 29715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19432 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) : 0.6272575 object centre at (A) : 34.73450 28.14350 31.04200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1041060E-02 5.7918350E-03 midg,1,midg; midg,igrid,midg -3.5024397E-02 3.0258827E-02 1,midg,midg; igrid,midg,midg 3.9550150E-03 9.8689077E-03 gauss-seidel spectral radius is 0.9985988 estimated iterations to convergence 212 setup time was (sec) 0.9500000 now iterating at: 00:32:31 rms-change max change #iterations 4.152374 183.6379 at 10iterations 1.910853 68.58050 at 20iterations 0.8876026 29.90683 at 30iterations 0.4122714 13.61915 at 40iterations 0.1912760 6.107370 at 50iterations 8.9025632E-02 3.127830 at 60iterations 4.1342143E-02 1.296076 at 70iterations 1.9304899E-02 0.5840263 at 80iterations 9.1067702E-03 0.2866421 at 90iterations 4.3605776E-03 0.1481628 at 100iterations 2.1438247E-03 7.9925537E-02 at 110iterations 1.1026919E-03 4.4498444E-02 at 120iterations finished qdiffx linear iterations at : 00:32:40 total time elapsed so far: 9.240000 # loops : 120 mean,max change (kT/e) : 1.1026919E-03 4.4498444E-02 energy calculations done at 9.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.430000 DelPhi exited at 00:32:40 9.431u 0.249s 0:10.24 94.4% 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 00:32:40 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 = 2620 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: 2.822659 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): 9.811001 59.65800 ymin,ymax (A): -0.2340000 56.52100 zmin,zma (A): 9.641000 52.44300 x,y,z range (A): 49.84700 56.75500 42.80200 scale (grids/A): 2.822659 object centre (A): 34.73450 28.14350 31.04200 number of atom coordinates read : 2620 total number of charged atoms : 2479 net assigned charge : 8.000013 assigned positive charge : 395.0007 centred at (gu) : 89.43318 94.34974 89.86896 assigned negative charge : -387.0014 centred at (gu) : 89.51768 93.44397 90.44308 start vw surface at 0.1700000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 170134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21429 grid for indexing accessible points = 1.400000 m= 86544 mr = 125465 m= 31815 mr = 71842 m= 7583 mr = 26235 m= 942 mr = 5937 m= 32 mr = 581 m= 0 mr = 11 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 7228 time to turn everything in is 1.550000 number of dielectric boundary points 66979 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 19831 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) : 1.881773 object centre at (A) : 34.73450 28.14350 31.04200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3125692 7.2509371E-02 midg,1,midg; midg,igrid,midg -0.7342262 0.1094608 1,midg,midg; igrid,midg,midg -9.2244176E-03 -1.7308722E-03 gauss-seidel spectral radius is 0.9992422 estimated iterations to convergence 287 setup time was (sec) 1.870000 now iterating at: 00:32:42 rms-change max change #iterations 9.720393 327.8343 at 10iterations 5.611396 135.2267 at 20iterations 3.210685 65.15766 at 30iterations 1.842434 35.83040 at 40iterations 1.055923 24.63771 at 50iterations 0.6014370 12.16050 at 60iterations 0.3446824 6.709930 at 70iterations 0.1968885 3.590157 at 80iterations 0.1125895 2.195452 at 90iterations 6.4401202E-02 1.256931 at 100iterations 3.6883578E-02 0.7256165 at 110iterations 2.1154799E-02 0.4345322 at 120iterations 1.2185487E-02 0.2507362 at 130iterations 7.0800437E-03 0.1422501 at 140iterations 4.1753883E-03 9.2147827E-02 at 150iterations 2.5297748E-03 6.6116333E-02 at 160iterations 1.5969296E-03 3.9474487E-02 at 170iterations 1.0656727E-03 2.6317596E-02 at 180iterations finished qdiffx linear iterations at : 00:32:56 total time elapsed so far: 14.92000 # loops : 180 mean,max change (kT/e) : 1.0656727E-03 2.6317596E-02 energy calculations done at 14.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.11000 DelPhi exited at 00:32:56 15.111u 0.284s 0:15.70 98.0% 0+0k 0+0io 0pf+0w