Sat Oct 8 11:38:28 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 11:38:28 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 = 4367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5637014 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): -27.65300 35.50100 ymin,ymax (A): 38.16500 95.72100 zmin,zma (A): 30.71700 90.31700 x,y,z range (A): 63.15400 57.55600 59.60000 scale (grids/A): 0.5637014 object centre (A): 3.924002 66.94300 60.51700 number of atom coordinates read : 4367 total number of charged atoms : 4207 net assigned charge : -5.499949 assigned positive charge : 655.6423 centred at (gu) : 90.91057 88.67121 89.12247 assigned negative charge : -661.1454 centred at (gu) : 90.80434 88.75328 89.30684 start vw surface at 0.2500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 8809 nv = 96 ne = 84 npr = 92028 no. pairs analyzed = 92028 no. exposed pairs = 4890 no. arc points = 33263 no. surface atoms = 1645 nbur = 2722 mkacc time = 0.2600000 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 = 1.540000 m= 370 mr = 5120 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.2899999 no. cavity mid-points inaccessible to solvent = 82 time to turn everything in is 0.5800000 number of dielectric boundary points 4024 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3447 ## 444 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 11598 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2786227E-09 -3.4562531E-09 midg,1,midg; midg,igrid,midg 1.0985505E-09 -1.6685797E-09 1,midg,midg; igrid,midg,midg -2.2141109E-09 1.5392247E-09 gauss-seidel spectral radius is 0.9838591 estimated iterations to convergence 65 setup time was (sec) 0.8600000 now iterating at: 11:38:29 rms-change max change #iterations 0.1068384 19.39984 at 10iterations 9.2715845E-03 1.260071 at 20iterations 1.7925635E-03 0.2448635 at 30iterations 6.1877584E-04 7.7960968E-02 at 40iterations 2.4438088E-04 3.4120560E-02 at 50iterations finished qdiffx linear iterations at : 11:38:32 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 2.4438088E-04 3.4120560E-02 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 11:38:33 4.327u 0.180s 0:04.99 90.1% 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 11:38:33 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 = 4367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.691104 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): -27.65300 35.50100 ymin,ymax (A): 38.16500 95.72100 zmin,zma (A): 30.71700 90.31700 x,y,z range (A): 63.15400 57.55600 59.60000 scale (grids/A): 1.691104 object centre (A): 3.924002 66.94300 60.51700 number of atom coordinates read : 4367 total number of charged atoms : 4207 net assigned charge : -5.499949 assigned positive charge : 655.6423 centred at (gu) : 92.73025 86.01237 87.36656 assigned negative charge : -661.1454 centred at (gu) : 92.41250 86.25925 87.92023 start vw surface at 0.2300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 97617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33263 grid for indexing accessible points = 1.400000 m= 33875 mr = 70669 m= 4084 mr = 25415 m= 124 mr = 2412 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 5511 time to turn everything in is 0.9100000 number of dielectric boundary points 37184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 321 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 32472 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) : 0.5637014 object centre at (A) : 3.924002 66.94300 60.51700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0232480E-02 -2.6426708E-02 midg,1,midg; midg,igrid,midg 1.9970872E-02 -1.0377077E-02 1,midg,midg; igrid,midg,midg -2.3594936E-02 2.5544109E-02 gauss-seidel spectral radius is 0.9984283 estimated iterations to convergence 200 setup time was (sec) 1.280000 now iterating at: 11:38:35 rms-change max change #iterations 4.492187 172.7650 at 10iterations 1.992106 77.87252 at 20iterations 0.8869771 27.14694 at 30iterations 0.3944971 11.57936 at 40iterations 0.1749519 5.626873 at 50iterations 7.8120291E-02 2.445820 at 60iterations 3.4998752E-02 1.037056 at 70iterations 1.5858129E-02 0.4746590 at 80iterations 7.3361089E-03 0.2208633 at 90iterations 3.5676428E-03 0.1063881 at 100iterations 1.9044882E-03 6.0295105E-02 at 110iterations 1.1357369E-03 3.4606934E-02 at 120iterations finished qdiffx linear iterations at : 11:38:43 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 1.1357369E-03 3.4606934E-02 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.420000 DelPhi exited at 11:38:44 9.423u 0.275s 0:10.23 94.7% 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 Sat Oct 8 2011 at 11:38:44 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 = 4367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.536656 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): -27.65300 35.50100 ymin,ymax (A): 38.16500 95.72100 zmin,zma (A): 30.71700 90.31700 x,y,z range (A): 63.15400 57.55600 59.60000 scale (grids/A): 2.536656 object centre (A): 3.924002 66.94300 60.51700 number of atom coordinates read : 4367 total number of charged atoms : 4207 net assigned charge : -5.499949 assigned positive charge : 655.6423 centred at (gu) : 94.09525 84.01816 86.04941 assigned negative charge : -661.1454 centred at (gu) : 93.61864 84.38886 86.88020 start vw surface at 0.2400000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 226570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33263 grid for indexing accessible points = 1.400000 m= 113379 mr = 171191 m= 37062 mr = 93916 m= 6957 mr = 30187 m= 593 mr = 5092 m= 16 mr = 341 m= 0 mr = 0 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 18595 time to turn everything in is 2.100000 number of dielectric boundary points 83850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 2.270000 number of grid points assigned charge 33631 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) : 1.691104 object centre at (A) : 3.924002 66.94300 60.51700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6914620 -0.3340835 midg,1,midg; midg,igrid,midg 0.3101686 -0.2291771 1,midg,midg; igrid,midg,midg -0.2561290 0.3445036 gauss-seidel spectral radius is 0.9992263 estimated iterations to convergence 284 setup time was (sec) 2.470000 now iterating at: 11:38:46 rms-change max change #iterations 11.21932 306.1026 at 10iterations 6.483397 128.7493 at 20iterations 3.723802 68.70573 at 30iterations 2.138366 40.60098 at 40iterations 1.221112 20.61760 at 50iterations 0.6989260 11.96958 at 60iterations 0.3985001 7.461655 at 70iterations 0.2274560 3.820534 at 80iterations 0.1297064 2.166792 at 90iterations 7.3927984E-02 1.396271 at 100iterations 4.2181682E-02 0.7037115 at 110iterations 2.4280483E-02 0.4569941 at 120iterations 1.4036374E-02 0.2445221 at 130iterations 8.2672155E-03 0.1441345 at 140iterations 5.0134794E-03 9.2904091E-02 at 150iterations 3.1851456E-03 6.0607910E-02 at 160iterations 2.1503482E-03 3.7162781E-02 at 170iterations 1.5466210E-03 3.0244827E-02 at 180iterations finished qdiffx linear iterations at : 11:38:59 total time elapsed so far: 15.03000 # loops : 180 mean,max change (kT/e) : 1.5466210E-03 3.0244827E-02 energy calculations done at 15.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.26000 DelPhi exited at 11:38:59 15.261u 0.208s 0:15.77 98.0% 0+0k 0+0io 0pf+0w