Sat Oct 8 12:16:18 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 Sat Oct 8 2011 at 12:16:18 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 = 3108 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: 0.6010062 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): -14.59400 44.64000 ymin,ymax (A): -12.60300 45.81900 zmin,zma (A): -5.200000 52.71400 x,y,z range (A): 59.23400 58.42200 57.91400 scale (grids/A): 0.6010062 object centre (A): 15.02300 16.60800 23.75700 number of atom coordinates read : 3108 total number of charged atoms : 2970 net assigned charge : 3.000004 assigned positive charge : 428.1720 centred at (gu) : 89.04030 89.55356 88.55474 assigned negative charge : -425.1732 centred at (gu) : 88.90827 89.71317 88.59105 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7815 nv = 96 ne = 84 npr = 62598 no. pairs analyzed = 62598 no. exposed pairs = 4575 no. arc points = 32286 no. surface atoms = 1537 nbur = 1571 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 420 mr = 3544 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3084 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9428 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9182422E-09 -1.0163340E-10 midg,1,midg; midg,igrid,midg 8.6139700E-09 -4.8188387E-09 1,midg,midg; igrid,midg,midg -5.2385909E-09 5.3712039E-09 gauss-seidel spectral radius is 0.9857422 estimated iterations to convergence 69 setup time was (sec) 0.7200000 now iterating at: 12:16:19 rms-change max change #iterations 0.1107169 18.44453 at 10iterations 1.0642515E-02 1.564509 at 20iterations 2.5840618E-03 0.4384079 at 30iterations 1.1200329E-03 0.1969261 at 40iterations 5.0867983E-04 8.9633942E-02 at 50iterations finished qdiffx linear iterations at : 12:16:23 total time elapsed so far: 5.130000 # loops : 50 mean,max change (kT/e) : 5.0867983E-04 8.9633942E-02 energy calculations done at 5.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.300000 DelPhi exited at 12:16:24 5.306u 0.458s 0:06.09 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 Sat Oct 8 2011 at 12:16:24 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 = 3108 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: 1.803018 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): -14.59400 44.64000 ymin,ymax (A): -12.60300 45.81900 zmin,zma (A): -5.200000 52.71400 x,y,z range (A): 59.23400 58.42200 57.91400 scale (grids/A): 1.803018 object centre (A): 15.02300 16.60800 23.75700 number of atom coordinates read : 3108 total number of charged atoms : 2970 net assigned charge : 3.000004 assigned positive charge : 428.1720 centred at (gu) : 87.11962 88.65971 85.66330 assigned negative charge : -425.1732 centred at (gu) : 86.72475 89.13952 85.77279 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32286 grid for indexing accessible points = 1.400000 m= 27210 mr = 52508 m= 4047 mr = 17397 m= 209 mr = 2094 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 43255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 23217 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) : 0.6010062 object centre at (A) : 15.02300 16.60800 23.75700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9692054E-03 1.1081275E-02 midg,1,midg; midg,igrid,midg -8.1073761E-04 1.6145665E-03 1,midg,midg; igrid,midg,midg -1.4196025E-02 5.1260881E-02 gauss-seidel spectral radius is 0.9985712 estimated iterations to convergence 210 setup time was (sec) 1.080000 now iterating at: 12:16:26 rms-change max change #iterations 4.024973 185.4756 at 10iterations 1.832473 72.90343 at 20iterations 0.8404243 30.45222 at 30iterations 0.3858888 13.20873 at 40iterations 0.1772269 5.881139 at 50iterations 8.1619732E-02 2.776862 at 60iterations 3.7728567E-02 1.281952 at 70iterations 1.7802082E-02 0.5843658 at 80iterations 8.7944027E-03 0.2894859 at 90iterations 4.7319033E-03 0.1730042 at 100iterations 2.8583906E-03 0.1164551 at 110iterations 1.9561306E-03 7.0640564E-02 at 120iterations finished qdiffx linear iterations at : 12:16:37 total time elapsed so far: 12.63000 # loops : 120 mean,max change (kT/e) : 1.9561306E-03 7.0640564E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 12:16:38 12.798u 0.532s 0:13.64 97.6% 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 8 2011 at 12:16:38 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 = 3108 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: 2.704528 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): -14.59400 44.64000 ymin,ymax (A): -12.60300 45.81900 zmin,zma (A): -5.200000 52.71400 x,y,z range (A): 59.23400 58.42200 57.91400 scale (grids/A): 2.704528 object centre (A): 15.02300 16.60800 23.75700 number of atom coordinates read : 3108 total number of charged atoms : 2970 net assigned charge : 3.000004 assigned positive charge : 428.1720 centred at (gu) : 85.67937 87.98929 83.49477 assigned negative charge : -425.1732 centred at (gu) : 85.08704 88.70920 83.65896 start vw surface at 0.1300000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 194036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32286 grid for indexing accessible points = 1.400000 m= 88317 mr = 129776 m= 30317 mr = 66267 m= 6871 mr = 21855 m= 806 mr = 4527 m= 32 mr = 387 m= 0 mr = 1 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.850000 number of dielectric boundary points 97566 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 23758 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) : 1.803018 object centre at (A) : 15.02300 16.60800 23.75700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8049708E-02 0.1171618 midg,1,midg; midg,igrid,midg -0.1178961 -2.5633959E-02 1,midg,midg; igrid,midg,midg -0.5589967 0.7018819 gauss-seidel spectral radius is 0.9992783 estimated iterations to convergence 294 setup time was (sec) 2.260000 now iterating at: 12:16:41 rms-change max change #iterations 10.04922 311.9376 at 10iterations 6.108584 162.3087 at 20iterations 3.676817 86.05180 at 30iterations 2.190005 60.47700 at 40iterations 1.297702 26.04972 at 50iterations 0.7662114 15.19246 at 60iterations 0.4504451 9.981089 at 70iterations 0.2642559 5.458071 at 80iterations 0.1544610 2.904190 at 90iterations 9.0337336E-02 1.753517 at 100iterations 5.2849296E-02 0.9793301 at 110iterations 3.0852035E-02 0.6362801 at 120iterations 1.8119419E-02 0.3141785 at 130iterations 1.0708932E-02 0.2277234 at 140iterations 6.4489944E-03 0.1366081 at 150iterations 4.0131477E-03 7.7461243E-02 at 160iterations 2.6352326E-03 5.6617737E-02 at 170iterations 1.8610521E-03 4.0325165E-02 at 180iterations finished qdiffx linear iterations at : 12:17:00 total time elapsed so far: 22.04000 # loops : 180 mean,max change (kT/e) : 1.8610521E-03 4.0325165E-02 energy calculations done at 22.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.22000 DelPhi exited at 12:17:01 22.222u 0.578s 0:23.11 98.6% 0+0k 0+0io 0pf+0w