Mon Oct 10 17:04:00 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 17:04:00 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5228 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5062283 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): -18.87100 37.01800 ymin,ymax (A): -30.76500 32.36600 zmin,zma (A): -3.940000 66.38400 x,y,z range (A): 55.88900 63.13100 70.32400 scale (grids/A): 0.5062283 object centre (A): 9.073501 0.8004999 31.22200 number of atom coordinates read : 5228 total number of charged atoms : 4972 net assigned charge : 5.706027 assigned positive charge : 787.0404 centred at (gu) : 90.51664 90.76434 89.41062 assigned negative charge : -781.3397 centred at (gu) : 90.44029 90.78477 89.40157 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8400 nv = 96 ne = 84 npr = 106661 no. pairs analyzed = 106661 no. exposed pairs = 6422 no. arc points = 44516 no. surface atoms = 2181 nbur = 3047 mkacc time = 0.3000000 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 = 1.680000 m= 305 mr = 4423 m= 0 mr = 11 time to grow re-entrant surface = 0.3399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 4271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4318 ## 671 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 11231 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1924229E-11 7.4839149E-11 midg,1,midg; midg,igrid,midg 9.3221750E-11 2.1247781E-11 1,midg,midg; igrid,midg,midg -9.9906056E-11 2.7959532E-10 gauss-seidel spectral radius is 0.9800742 estimated iterations to convergence 59 setup time was (sec) 0.8400000 now iterating at: 17:04:02 rms-change max change #iterations 6.9175705E-02 10.22778 at 10iterations 4.2774943E-03 0.6093597 at 20iterations 6.1537512E-04 8.9698792E-02 at 30iterations 1.9349261E-04 2.1690369E-02 at 40iterations 6.9531343E-05 7.9584122E-03 at 50iterations finished qdiffx linear iterations at : 17:04:05 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 6.9531343E-05 7.9584122E-03 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 17:04:06 4.318u 0.286s 0:05.27 87.0% 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 17:04:06 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5228 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.518685 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): -18.87100 37.01800 ymin,ymax (A): -30.76500 32.36600 zmin,zma (A): -3.940000 66.38400 x,y,z range (A): 55.88900 63.13100 70.32400 scale (grids/A): 1.518685 object centre (A): 9.073501 0.8004999 31.22200 number of atom coordinates read : 5228 total number of charged atoms : 4972 net assigned charge : 5.706027 assigned positive charge : 787.0404 centred at (gu) : 91.54856 92.29152 88.23019 assigned negative charge : -781.3397 centred at (gu) : 91.32066 92.35381 88.20446 start vw surface at 0.2300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 95722 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44516 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27439 mr = 66613 m= 2422 mr = 17945 m= 68 mr = 1003 m= 0 mr = 2 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8500000 number of dielectric boundary points 40088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 583 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 37233 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) : 0.5062283 object centre at (A) : 9.073501 0.8004999 31.22200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5814430E-03 1.4434742E-02 midg,1,midg; midg,igrid,midg -3.7765127E-04 -1.3648090E-02 1,midg,midg; igrid,midg,midg -1.6222639E-03 1.0834659E-02 gauss-seidel spectral radius is 0.9981134 estimated iterations to convergence 183 setup time was (sec) 1.150000 now iterating at: 17:04:07 rms-change max change #iterations 3.932326 158.4159 at 10iterations 1.613594 55.54002 at 20iterations 0.6622739 23.13983 at 30iterations 0.2725962 8.655558 at 40iterations 0.1116235 3.477944 at 50iterations 4.5745477E-02 1.532829 at 60iterations 1.8890381E-02 0.5632629 at 70iterations 7.7825179E-03 0.2383032 at 80iterations 3.2197630E-03 9.4711304E-02 at 90iterations 1.3525576E-03 4.3453217E-02 at 100iterations 5.8598036E-04 1.7029762E-02 at 110iterations 2.7329667E-04 8.9073181E-03 at 120iterations finished qdiffx linear iterations at : 17:04:16 total time elapsed so far: 9.590000 # loops : 120 mean,max change (kT/e) : 2.7329667E-04 8.9073181E-03 energy calculations done at 9.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.770000 DelPhi exited at 17:04:16 9.771u 0.307s 0:10.39 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 Mon Oct 10 2011 at 17:04:16 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5228 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.278028 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): -18.87100 37.01800 ymin,ymax (A): -30.76500 32.36600 zmin,zma (A): -3.940000 66.38400 x,y,z range (A): 55.88900 63.13100 70.32400 scale (grids/A): 2.278028 object centre (A): 9.073501 0.8004999 31.22200 number of atom coordinates read : 5228 total number of charged atoms : 4972 net assigned charge : 5.706027 assigned positive charge : 787.0404 centred at (gu) : 92.32243 93.43712 87.34492 assigned negative charge : -781.3397 centred at (gu) : 91.98088 93.53078 87.30663 start vw surface at 0.2300000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 223599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44516 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 98980 mr = 163613 m= 24435 mr = 77206 m= 3447 mr = 17228 m= 196 mr = 1990 m= 4 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.090000 number of dielectric boundary points 90557 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 2.250000 number of grid points assigned charge 39652 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) : 1.518685 object centre at (A) : 9.073501 0.8004999 31.22200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1623655 0.2732960 midg,1,midg; midg,igrid,midg -7.7677429E-02 -0.3383658 1,midg,midg; igrid,midg,midg -2.5017569E-02 0.1620861 gauss-seidel spectral radius is 0.9991721 estimated iterations to convergence 274 setup time was (sec) 2.430000 now iterating at: 17:04:19 rms-change max change #iterations 10.72702 256.3957 at 10iterations 6.165758 153.3372 at 20iterations 3.525085 73.95130 at 30iterations 2.003299 40.50078 at 40iterations 1.133079 24.34691 at 50iterations 0.6382544 13.37482 at 60iterations 0.3590017 6.627993 at 70iterations 0.2014161 4.056229 at 80iterations 0.1127635 2.137714 at 90iterations 6.3142836E-02 1.153130 at 100iterations 3.5337377E-02 0.7322006 at 110iterations 1.9690653E-02 0.3631287 at 120iterations 1.1020422E-02 0.2030754 at 130iterations 6.1520697E-03 0.1160434 at 140iterations 3.4337002E-03 6.1010361E-02 at 150iterations 1.9169713E-03 3.4053802E-02 at 160iterations 1.0744089E-03 2.0133972E-02 at 170iterations 6.0243008E-04 1.1710658E-02 at 180iterations finished qdiffx linear iterations at : 17:04:33 total time elapsed so far: 16.59000 # loops : 180 mean,max change (kT/e) : 6.0243008E-04 1.1710658E-02 energy calculations done at 16.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.77000 DelPhi exited at 17:04:34 16.771u 0.315s 0:17.81 95.9% 0+0k 0+0io 0pf+0w