Mon Oct 10 11:47:35 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+sph2.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 = amb2.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 Mon Oct 10 2011 at 11:47:35 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2095 !!! WARNING: GLU 223 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7448010 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): 41.63200 89.43000 ymin,ymax (A): 6.234000 53.64300 zmin,zma (A): 5.425000 52.71300 x,y,z range (A): 47.79800 47.40900 47.28800 scale (grids/A): 0.7448010 object centre (A): 65.53100 29.93850 29.06900 number of atom coordinates read : 2095 total number of charged atoms : 1957 net assigned charge : -5.999990 assigned positive charge : 313.1720 centred at (gu) : 89.15048 90.07490 90.22287 assigned negative charge : -319.1720 centred at (gu) : 89.10050 90.00719 90.08205 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8040 nv = 96 ne = 84 npr = 42645 no. pairs analyzed = 42645 no. exposed pairs = 2675 no. arc points = 18562 no. surface atoms = 907 nbur = 1188 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 551 mr = 4493 m= 4 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.3200000 number of dielectric boundary points 3994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1525 ## 118 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8447 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6511407E-07 4.0102311E-08 midg,1,midg; midg,igrid,midg -1.9042099E-07 -4.2382176E-08 1,midg,midg; igrid,midg,midg -2.0229487E-07 -5.3302315E-08 gauss-seidel spectral radius is 0.9906050 estimated iterations to convergence 84 setup time was (sec) 0.6400000 now iterating at: 11:47:36 rms-change max change #iterations 0.2484272 33.85990 at 10iterations 3.4315806E-02 4.597949 at 20iterations 4.6447399E-03 0.5431060 at 30iterations 6.3682772E-04 8.9319229E-02 at 40iterations 8.7177956E-05 1.2901306E-02 at 50iterations finished qdiffx linear iterations at : 11:47:39 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 8.7177956E-05 1.2901306E-02 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 11:47:40 4.267u 0.261s 0:05.07 89.1% 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 Mon Oct 10 2011 at 11:47:40 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2095 !!! WARNING: GLU 223 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.234403 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): 41.63200 89.43000 ymin,ymax (A): 6.234000 53.64300 zmin,zma (A): 5.425000 52.71300 x,y,z range (A): 47.79800 47.40900 47.28800 scale (grids/A): 2.234403 object centre (A): 65.53100 29.93850 29.06900 number of atom coordinates read : 2095 total number of charged atoms : 1957 net assigned charge : -5.999990 assigned positive charge : 313.1720 centred at (gu) : 87.45160 90.22441 90.66844 assigned negative charge : -319.1720 centred at (gu) : 87.30153 90.02163 90.24617 start vw surface at 0.1800000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 84604 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18562 grid for indexing accessible points = 1.400000 m= 34128 mr = 58698 m= 7491 mr = 25974 m= 815 mr = 5295 m= 25 mr = 464 m= 0 mr = 4 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 508 time to turn everything in is 0.8200000 number of dielectric boundary points 36628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 46 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 15595 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) : 0.7448010 object centre at (A) : 65.53100 29.93850 29.06900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1101791 1.4731470E-02 midg,1,midg; midg,igrid,midg -4.5843858E-02 -3.3445649E-02 1,midg,midg; igrid,midg,midg -2.5997218E-02 5.3891838E-03 gauss-seidel spectral radius is 0.9989363 estimated iterations to convergence 243 setup time was (sec) 1.160000 now iterating at: 11:47:42 rms-change max change #iterations 5.141881 221.3120 at 10iterations 2.610362 96.36714 at 20iterations 1.336172 38.21830 at 30iterations 0.6831268 18.57859 at 40iterations 0.3488093 9.826952 at 50iterations 0.1790447 5.726183 at 60iterations 9.1829546E-02 2.646141 at 70iterations 4.6805184E-02 1.261471 at 80iterations 2.3897668E-02 0.6656895 at 90iterations 1.2267874E-02 0.3493500 at 100iterations 6.2639141E-03 0.1696157 at 110iterations 3.2063050E-03 8.6255074E-02 at 120iterations finished qdiffx linear iterations at : 11:47:50 total time elapsed so far: 9.750000 # loops : 120 mean,max change (kT/e) : 3.2063050E-03 8.6255074E-02 energy calculations done at 9.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.930000 DelPhi exited at 11:47:51 9.932u 0.252s 0:10.58 96.2% 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 Mon Oct 10 2011 at 11:47:51 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2095 !!! WARNING: GLU 223 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.351605 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): 41.63200 89.43000 ymin,ymax (A): 6.234000 53.64300 zmin,zma (A): 5.425000 52.71300 x,y,z range (A): 47.79800 47.40900 47.28800 scale (grids/A): 3.351605 object centre (A): 65.53100 29.93850 29.06900 number of atom coordinates read : 2095 total number of charged atoms : 1957 net assigned charge : -5.999990 assigned positive charge : 313.1720 centred at (gu) : 86.17733 90.33680 91.00277 assigned negative charge : -319.1720 centred at (gu) : 85.95229 90.03255 90.36923 start vw surface at 0.1600000 fill in re-entrant regions at 1.060000 boundary points on vw surface= 194805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18562 grid for indexing accessible points = 1.400000 m= 104088 mr = 141329 m= 44902 mr = 86465 m= 14583 mr = 37335 m= 3455 mr = 11700 m= 449 mr = 2690 m= 23 mr = 300 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 1710 time to turn everything in is 2.270000 number of dielectric boundary points 82475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.430000 number of grid points assigned charge 15656 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) : 2.234403 object centre at (A) : 65.53100 29.93850 29.06900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.074216 0.1986279 midg,1,midg; midg,igrid,midg -0.2445787 -0.2843912 1,midg,midg; igrid,midg,midg -0.2203038 -5.4168619E-02 gauss-seidel spectral radius is 0.9993201 estimated iterations to convergence 303 setup time was (sec) 2.620000 now iterating at: 11:47:54 rms-change max change #iterations 11.06523 337.6750 at 10iterations 6.512665 148.3025 at 20iterations 3.841956 70.71558 at 30iterations 2.262453 41.91702 at 40iterations 1.330990 21.65128 at 50iterations 0.7841165 14.11574 at 60iterations 0.4607066 7.893614 at 70iterations 0.2715065 4.345359 at 80iterations 0.1592031 2.576577 at 90iterations 9.3827613E-02 1.552212 at 100iterations 5.5127971E-02 0.8579187 at 110iterations 3.2363471E-02 0.4946289 at 120iterations 1.9029869E-02 0.2882118 at 130iterations 1.1167123E-02 0.1765623 at 140iterations 6.5714391E-03 0.1147945 at 150iterations 3.8628802E-03 6.4317703E-02 at 160iterations 2.2641995E-03 3.8513184E-02 at 170iterations 1.3346610E-03 2.0082474E-02 at 180iterations finished qdiffx linear iterations at : 11:48:07 total time elapsed so far: 16.23000 # loops : 180 mean,max change (kT/e) : 1.3346610E-03 2.0082474E-02 energy calculations done at 16.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.41000 DelPhi exited at 11:48:08 16.409u 0.288s 0:17.16 97.2% 0+0k 0+0io 0pf+0w