Sat Oct 8 14:07:47 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 14:07:47 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2980 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6395975 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): -12.27600 43.38400 ymin,ymax (A): -22.95600 22.74800 zmin,zma (A): -7.586000 47.51800 x,y,z range (A): 55.66000 45.70400 55.10400 scale (grids/A): 0.6395975 object centre (A): 15.55400 -0.1040001 19.96600 number of atom coordinates read : 2980 total number of charged atoms : 2835 net assigned charge : 1.500007 assigned positive charge : 446.1956 centred at (gu) : 88.75880 89.59725 91.77671 assigned negative charge : -444.6964 centred at (gu) : 88.69322 89.46795 91.76358 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8107 nv = 96 ne = 84 npr = 62541 no. pairs analyzed = 62541 no. exposed pairs = 3307 no. arc points = 23205 no. surface atoms = 1127 nbur = 1853 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 4752 m= 0 mr = 50 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3500000 number of dielectric boundary points 3702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2280 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9840 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3656789E-10 5.9266285E-09 midg,1,midg; midg,igrid,midg -1.6305357E-08 1.7494466E-08 1,midg,midg; igrid,midg,midg -8.4008027E-09 8.3430027E-09 gauss-seidel spectral radius is 0.9873621 estimated iterations to convergence 73 setup time was (sec) 0.6400000 now iterating at: 14:07:48 rms-change max change #iterations 0.1535848 22.89428 at 10iterations 1.5596068E-02 2.498009 at 20iterations 1.6318521E-03 0.1995697 at 30iterations 1.9698679E-04 2.6807785E-02 at 40iterations 2.8919423E-05 4.6319962E-03 at 50iterations finished qdiffx linear iterations at : 14:07:52 total time elapsed so far: 4.960000 # loops : 50 mean,max change (kT/e) : 2.8919423E-05 4.6319962E-03 energy calculations done at 4.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.130000 DelPhi exited at 14:07:53 5.130u 0.460s 0:05.88 95.0% 0+0k 0+0io 6pf+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 14:07:53 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2980 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.918792 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): -12.27600 43.38400 ymin,ymax (A): -22.95600 22.74800 zmin,zma (A): -7.586000 47.51800 x,y,z range (A): 55.66000 45.70400 55.10400 scale (grids/A): 1.918792 object centre (A): 15.55400 -0.1040001 19.96600 number of atom coordinates read : 2980 total number of charged atoms : 2835 net assigned charge : 1.500007 assigned positive charge : 446.1956 centred at (gu) : 86.27566 88.79117 95.32948 assigned negative charge : -444.6964 centred at (gu) : 86.07926 88.40360 95.29057 start vw surface at 0.1200000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 88263 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23205 grid for indexing accessible points = 1.400000 m= 31928 mr = 64151 m= 4804 mr = 24239 m= 296 mr = 3021 m= 3 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 1180 time to turn everything in is 0.7100000 number of dielectric boundary points 33768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 22324 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) : 0.6395975 object centre at (A) : 15.55400 -0.1040001 19.96600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1264060E-02 1.3742993E-02 midg,1,midg; midg,igrid,midg -3.4669039E-03 2.4510140E-02 1,midg,midg; igrid,midg,midg -3.2076627E-02 1.8821934E-02 gauss-seidel spectral radius is 0.9986818 estimated iterations to convergence 218 setup time was (sec) 1.060000 now iterating at: 14:07:54 rms-change max change #iterations 4.658394 215.7088 at 10iterations 2.224046 67.08479 at 20iterations 1.052716 30.09637 at 30iterations 0.5030030 14.91458 at 40iterations 0.2380639 7.650819 at 50iterations 0.1132645 3.302963 at 60iterations 5.4007560E-02 1.585445 at 70iterations 2.5654621E-02 0.7450075 at 80iterations 1.2202203E-02 0.3278623 at 90iterations 5.8025792E-03 0.1839600 at 100iterations 2.7598201E-03 8.6324453E-02 at 110iterations 1.3174823E-03 3.9440155E-02 at 120iterations finished qdiffx linear iterations at : 14:08:06 total time elapsed so far: 13.08000 # loops : 120 mean,max change (kT/e) : 1.3174823E-03 3.9440155E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.25000 DelPhi exited at 14:08:07 13.255u 0.522s 0:14.20 96.9% 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 14:08:07 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2980 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.878189 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): -12.27600 43.38400 ymin,ymax (A): -22.95600 22.74800 zmin,zma (A): -7.586000 47.51800 x,y,z range (A): 55.66000 45.70400 55.10400 scale (grids/A): 2.878189 object centre (A): 15.55400 -0.1040001 19.96600 number of atom coordinates read : 2980 total number of charged atoms : 2835 net assigned charge : 1.500007 assigned positive charge : 446.1956 centred at (gu) : 84.41342 88.18653 97.99416 assigned negative charge : -444.6964 centred at (gu) : 84.11885 87.60539 97.93597 start vw surface at 0.1300000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 204676 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23205 grid for indexing accessible points = 1.400000 m= 104839 mr = 154751 m= 36771 mr = 88030 m= 8511 mr = 29926 m= 1253 mr = 6304 m= 83 mr = 864 m= 0 mr = 35 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 3842 time to turn everything in is 1.920000 number of dielectric boundary points 76223 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 22676 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) : 1.918792 object centre at (A) : 15.55400 -0.1040001 19.96600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3058427E-02 0.3022301 midg,1,midg; midg,igrid,midg -2.5125848E-02 0.2749373 1,midg,midg; igrid,midg,midg -0.5295190 0.2356647 gauss-seidel spectral radius is 0.9992737 estimated iterations to convergence 293 setup time was (sec) 2.310000 now iterating at: 14:08:10 rms-change max change #iterations 10.78919 336.3813 at 10iterations 6.304512 154.9946 at 20iterations 3.658595 67.18234 at 30iterations 2.124992 44.82341 at 40iterations 1.230954 20.56796 at 50iterations 0.7132623 13.30555 at 60iterations 0.4120810 7.190113 at 70iterations 0.2385551 4.244480 at 80iterations 0.1377603 2.274714 at 90iterations 7.9765178E-02 1.327919 at 100iterations 4.6080694E-02 0.7901611 at 110iterations 2.6651692E-02 0.4452724 at 120iterations 1.5403997E-02 0.2645651 at 130iterations 8.9232204E-03 0.1735954 at 140iterations 5.1440089E-03 9.0898752E-02 at 150iterations 2.9836900E-03 5.0384521E-02 at 160iterations 1.7305941E-03 2.9911041E-02 at 170iterations 1.0047682E-03 1.6376495E-02 at 180iterations finished qdiffx linear iterations at : 14:08:28 total time elapsed so far: 21.14000 # loops : 180 mean,max change (kT/e) : 1.0047682E-03 1.6376495E-02 energy calculations done at 21.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.31000 DelPhi exited at 14:08:29 21.315u 0.538s 0:22.12 98.7% 0+0k 0+0io 0pf+0w