Sat Oct 8 21:20:08 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 21:20:08 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6150337 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): -31.41900 17.41700 ymin,ymax (A): -23.66900 22.51300 zmin,zma (A): -12.50300 45.38000 x,y,z range (A): 48.83600 46.18200 57.88300 scale (grids/A): 0.6150337 object centre (A): -7.001000 -0.5779991 16.43850 number of atom coordinates read : 2573 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.49156 89.28221 89.55084 assigned negative charge : -387.4045 centred at (gu) : 88.38696 89.33640 89.44956 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6299 nv = 96 ne = 84 npr = 53521 no. pairs analyzed = 53521 no. exposed pairs = 3010 no. arc points = 21952 no. surface atoms = 996 nbur = 1577 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 291 mr = 3474 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 126 time to turn everything in is 0.2000000 number of dielectric boundary points 3091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2206 ## 239 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7924 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3274290E-09 7.7795574E-09 midg,1,midg; midg,igrid,midg 6.9743140E-09 -1.9250768E-10 1,midg,midg; igrid,midg,midg -4.5657829E-09 6.2967360E-09 gauss-seidel spectral radius is 0.9863052 estimated iterations to convergence 70 setup time was (sec) 0.3800000 now iterating at: 21:20:08 rms-change max change #iterations 0.1217425 18.46771 at 10iterations 1.0977957E-02 1.658812 at 20iterations 9.7924483E-04 0.1341705 at 30iterations 8.7258908E-05 1.3320923E-02 at 40iterations 8.0388663E-06 1.2531281E-03 at 50iterations finished qdiffx linear iterations at : 21:20:11 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 8.0388663E-06 1.2531281E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 21:20:12 3.353u 0.176s 0:03.80 92.6% 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 21:20:12 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.845101 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): -31.41900 17.41700 ymin,ymax (A): -23.66900 22.51300 zmin,zma (A): -12.50300 45.38000 x,y,z range (A): 48.83600 46.18200 57.88300 scale (grids/A): 1.845101 object centre (A): -7.001000 -0.5779991 16.43850 number of atom coordinates read : 2573 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.47428 87.84631 88.65202 assigned negative charge : -387.4045 centred at (gu) : 85.16066 88.00893 88.34819 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21952 grid for indexing accessible points = 1.400000 m= 22617 mr = 48059 m= 2901 mr = 16444 m= 138 mr = 1735 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 4049 time to turn everything in is 0.3500000 number of dielectric boundary points 28465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19221 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) : 0.6150337 object centre at (A) : -7.001000 -0.5779991 16.43850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4457331E-02 1.9184446E-02 midg,1,midg; midg,igrid,midg 1.2898400E-02 1.0347083E-03 1,midg,midg; igrid,midg,midg -7.4378275E-03 3.1307824E-02 gauss-seidel spectral radius is 0.9985427 estimated iterations to convergence 208 setup time was (sec) 0.5500000 now iterating at: 21:20:12 rms-change max change #iterations 3.977867 174.1023 at 10iterations 1.812869 62.93089 at 20iterations 0.8299489 31.82607 at 30iterations 0.3781258 14.09798 at 40iterations 0.1725832 5.894436 at 50iterations 7.9047531E-02 2.754276 at 60iterations 3.5990331E-02 1.158721 at 70iterations 1.6492449E-02 0.5183754 at 80iterations 7.5000087E-03 0.2913752 at 90iterations 3.4435713E-03 0.1120201 at 100iterations 1.5740546E-03 6.1937332E-02 at 110iterations 7.2029262E-04 2.9724121E-02 at 120iterations finished qdiffx linear iterations at : 21:20:20 total time elapsed so far: 8.300000 # loops : 120 mean,max change (kT/e) : 7.2029262E-04 2.9724121E-02 energy calculations done at 8.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.440000 DelPhi exited at 21:20:21 8.441u 0.223s 0:08.96 96.6% 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 21:20:21 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.767652 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): -31.41900 17.41700 ymin,ymax (A): -23.66900 22.51300 zmin,zma (A): -12.50300 45.38000 x,y,z range (A): 48.83600 46.18200 57.88300 scale (grids/A): 2.767652 object centre (A): -7.001000 -0.5779991 16.43850 number of atom coordinates read : 2573 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 83.21127 86.76932 87.97791 assigned negative charge : -387.4045 centred at (gu) : 82.74097 87.01332 87.52223 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 160144 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21952 grid for indexing accessible points = 1.400000 m= 76697 mr = 116474 m= 24283 mr = 62795 m= 4990 mr = 19172 m= 537 mr = 3601 m= 28 mr = 329 m= 0 mr = 7 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 13440 time to turn everything in is 0.8300000 number of dielectric boundary points 64301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 19628 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) : 1.845101 object centre at (A) : -7.001000 -0.5779991 16.43850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1934521E-02 0.2201926 midg,1,midg; midg,igrid,midg 0.1675683 -1.4534455E-02 1,midg,midg; igrid,midg,midg -7.3327579E-02 0.4124621 gauss-seidel spectral radius is 0.9992272 estimated iterations to convergence 284 setup time was (sec) 1.060000 now iterating at: 21:20:22 rms-change max change #iterations 9.330374 341.4195 at 10iterations 5.339649 121.2986 at 20iterations 3.040538 78.49272 at 30iterations 1.731528 37.43592 at 40iterations 0.9828284 22.32173 at 50iterations 0.5587640 11.34981 at 60iterations 0.3167933 6.206320 at 70iterations 0.1794075 3.607397 at 80iterations 0.1020553 1.972008 at 90iterations 5.7765797E-02 1.137638 at 100iterations 3.2832611E-02 0.6237411 at 110iterations 1.8604891E-02 0.3457708 at 120iterations 1.0548795E-02 0.1947584 at 130iterations 5.9812735E-03 0.1282806 at 140iterations 3.3960592E-03 5.9477523E-02 at 150iterations 1.9298453E-03 3.6581993E-02 at 160iterations 1.0920076E-03 2.1684647E-02 at 170iterations 6.2011759E-04 1.2160063E-02 at 180iterations finished qdiffx linear iterations at : 21:20:33 total time elapsed so far: 12.06000 # loops : 180 mean,max change (kT/e) : 6.2011759E-04 1.2160063E-02 energy calculations done at 12.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 21:20:33 12.193u 0.246s 0:12.74 97.5% 0+0k 0+0io 0pf+0w