Mon Oct 10 16:02:39 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 16:02:39 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4765 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: ASP 610 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5507170 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): 7.795000 62.83800 ymin,ymax (A): 52.47100 117.0760 zmin,zma (A): -35.42600 29.21700 x,y,z range (A): 55.04300 64.60501 64.64301 scale (grids/A): 0.5507170 object centre (A): 35.31650 84.77350 -3.104502 number of atom coordinates read : 4765 total number of charged atoms : 4603 net assigned charge : 4.906020 assigned positive charge : 719.8517 centred at (gu) : 89.56835 89.97041 91.54029 assigned negative charge : -714.9500 centred at (gu) : 89.53237 90.00895 91.56275 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 9273 nv = 96 ne = 84 npr = 97395 no. pairs analyzed = 97395 no. exposed pairs = 5755 no. arc points = 39183 no. surface atoms = 1941 nbur = 2824 mkacc time = 0.1700000 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 = 1.568000 m= 397 mr = 5177 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3976 ## 512 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 12254 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5369625E-10 1.1832965E-10 midg,1,midg; midg,igrid,midg 8.6674684E-10 -1.1796053E-10 1,midg,midg; igrid,midg,midg -9.8024054E-11 7.4539774E-10 gauss-seidel spectral radius is 0.9831272 estimated iterations to convergence 63 setup time was (sec) 0.5100000 now iterating at: 16:02:39 rms-change max change #iterations 0.1013415 16.29631 at 10iterations 7.5645801E-03 0.9623027 at 20iterations 1.1665239E-03 0.2143440 at 30iterations 4.3173789E-04 7.1224213E-02 at 40iterations 1.8145081E-04 2.6081085E-02 at 50iterations finished qdiffx linear iterations at : 16:02:42 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 1.8145081E-04 2.6081085E-02 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 16:02:43 3.549u 0.170s 0:04.04 91.8% 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 16:02:43 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4765 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: ASP 610 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.652151 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): 7.795000 62.83800 ymin,ymax (A): 52.47100 117.0760 zmin,zma (A): -35.42600 29.21700 x,y,z range (A): 55.04300 64.60501 64.64301 scale (grids/A): 1.652151 object centre (A): 35.31650 84.77350 -3.104502 number of atom coordinates read : 4765 total number of charged atoms : 4603 net assigned charge : 4.906020 assigned positive charge : 719.8517 centred at (gu) : 88.70348 89.90961 94.61956 assigned negative charge : -714.9500 centred at (gu) : 88.59659 90.02644 94.68774 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 104568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39183 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 33984 mr = 74722 m= 3791 mr = 23976 m= 111 mr = 1975 m= 0 mr = 8 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1979 time to turn everything in is 0.5100000 number of dielectric boundary points 41773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 410 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 35351 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) : 0.5507170 object centre at (A) : 35.31650 84.77350 -3.104502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7085737E-03 1.4589563E-02 midg,1,midg; midg,igrid,midg 1.6765058E-02 1.7453266E-02 1,midg,midg; igrid,midg,midg 3.1065242E-04 4.9832263E-03 gauss-seidel spectral radius is 0.9984016 estimated iterations to convergence 198 setup time was (sec) 0.7400000 now iterating at: 16:02:44 rms-change max change #iterations 4.492268 167.0905 at 10iterations 1.972209 68.27962 at 20iterations 0.8700178 28.74654 at 30iterations 0.3829945 10.95632 at 40iterations 0.1689985 4.686339 at 50iterations 7.4479766E-02 2.239462 at 60iterations 3.3021927E-02 0.8765907 at 70iterations 1.4672001E-02 0.4185123 at 80iterations 6.6101393E-03 0.1940231 at 90iterations 3.1070479E-03 9.5438719E-02 at 100iterations 1.5402092E-03 4.6081543E-02 at 110iterations 8.6513878E-04 2.6702881E-02 at 120iterations finished qdiffx linear iterations at : 16:02:51 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 8.6513878E-04 2.6702881E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 16:02:51 8.094u 0.186s 0:08.77 94.2% 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 16:02:52 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4765 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: ASP 610 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.478226 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): 7.795000 62.83800 ymin,ymax (A): 52.47100 117.0760 zmin,zma (A): -35.42600 29.21700 x,y,z range (A): 55.04300 64.60501 64.64301 scale (grids/A): 2.478226 object centre (A): 35.31650 84.77350 -3.104502 number of atom coordinates read : 4765 total number of charged atoms : 4603 net assigned charge : 4.906020 assigned positive charge : 719.8517 centred at (gu) : 88.05490 89.86403 96.92885 assigned negative charge : -714.9500 centred at (gu) : 87.89465 90.03951 97.03158 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 243366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39183 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 116821 mr = 182290 m= 34737 mr = 93962 m= 6043 mr = 26647 m= 483 mr = 4106 m= 9 mr = 220 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 7055 time to turn everything in is 1.260000 number of dielectric boundary points 94234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 36792 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) : 1.652151 object centre at (A) : 35.31650 84.77350 -3.104502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1102598 0.5088364 midg,1,midg; midg,igrid,midg 0.1820001 0.3727953 1,midg,midg; igrid,midg,midg 2.7887931E-02 9.7842649E-02 gauss-seidel spectral radius is 0.9992399 estimated iterations to convergence 286 setup time was (sec) 1.510000 now iterating at: 16:02:53 rms-change max change #iterations 11.55119 316.6395 at 10iterations 6.803969 138.1057 at 20iterations 3.976409 83.88228 at 30iterations 2.317901 43.41592 at 40iterations 1.344551 27.29322 at 50iterations 0.7783942 14.10934 at 60iterations 0.4498132 8.231634 at 70iterations 0.2588046 4.448821 at 80iterations 0.1491085 2.528801 at 90iterations 8.5586026E-02 1.469042 at 100iterations 4.9140252E-02 0.8327932 at 110iterations 2.8213715E-02 0.4764967 at 120iterations 1.6204033E-02 0.2680359 at 130iterations 9.3052890E-03 0.1660156 at 140iterations 5.3677354E-03 8.9149475E-02 at 150iterations 3.1153867E-03 4.9549103E-02 at 160iterations 1.8262147E-03 3.1299591E-02 at 170iterations 1.0974531E-03 2.0599365E-02 at 180iterations finished qdiffx linear iterations at : 16:03:05 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 1.0974531E-03 2.0599365E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.45000 DelPhi exited at 16:03:06 13.450u 0.215s 0:14.33 95.3% 0+0k 0+0io 0pf+0w