Sat Oct 8 21:08:27 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 21:08:27 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 = 2606 !!! 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 595 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6186785 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): -32.12600 17.37300 ymin,ymax (A): -23.81100 23.20100 zmin,zma (A): -12.51100 45.03100 x,y,z range (A): 49.49900 47.01200 57.54200 scale (grids/A): 0.6186785 object centre (A): -7.376500 -0.3049994 16.26000 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.70715 89.09332 89.62116 assigned negative charge : -388.8955 centred at (gu) : 88.58791 89.14085 89.51671 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6495 nv = 96 ne = 84 npr = 54623 no. pairs analyzed = 54623 no. exposed pairs = 3048 no. arc points = 21600 no. surface atoms = 1018 nbur = 1588 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 311 mr = 3609 m= 0 mr = 32 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 76 time to turn everything in is 0.3200000 number of dielectric boundary points 3165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2156 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8111 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4669536E-09 9.3696872E-09 midg,1,midg; midg,igrid,midg 8.0683371E-09 4.6608811E-10 1,midg,midg; igrid,midg,midg -5.6190048E-09 8.3628464E-09 gauss-seidel spectral radius is 0.9864667 estimated iterations to convergence 70 setup time was (sec) 0.5400000 now iterating at: 21:08:28 rms-change max change #iterations 0.1231574 18.46346 at 10iterations 1.1489219E-02 1.482681 at 20iterations 1.0639512E-03 0.1617889 at 30iterations 9.8703793E-05 1.4732361E-02 at 40iterations 9.3269346E-06 1.2626648E-03 at 50iterations finished qdiffx linear iterations at : 21:08:30 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 9.3269346E-06 1.2626648E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 21:08:31 3.168u 0.157s 0:03.65 90.6% 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 21:08:31 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 = 2606 !!! 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 595 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.856035 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): -32.12600 17.37300 ymin,ymax (A): -23.81100 23.20100 zmin,zma (A): -12.51100 45.03100 x,y,z range (A): 49.49900 47.01200 57.54200 scale (grids/A): 1.856035 object centre (A): -7.376500 -0.3049994 16.26000 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 86.12085 87.27932 88.86287 assigned negative charge : -388.8955 centred at (gu) : 85.76337 87.42245 88.54985 start vw surface at 0.2300000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 71159 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21600 grid for indexing accessible points = 1.400000 m= 24347 mr = 49926 m= 3353 mr = 18080 m= 165 mr = 2024 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 5354 time to turn everything in is 0.5700000 number of dielectric boundary points 28940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 19324 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) : 0.6186785 object centre at (A) : -7.376500 -0.3049994 16.26000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6285548E-02 1.7132064E-02 midg,1,midg; midg,igrid,midg 1.4655805E-02 7.7505638E-03 1,midg,midg; igrid,midg,midg -7.8015202E-03 3.5845079E-02 gauss-seidel spectral radius is 0.9985602 estimated iterations to convergence 209 setup time was (sec) 0.8600000 now iterating at: 21:08:32 rms-change max change #iterations 3.998046 157.2328 at 10iterations 1.837950 70.03961 at 20iterations 0.8435794 31.96786 at 30iterations 0.3864857 12.39122 at 40iterations 0.1782168 5.721878 at 50iterations 8.1522204E-02 2.829060 at 60iterations 3.7534378E-02 1.323031 at 70iterations 1.7142799E-02 0.5782623 at 80iterations 7.8787059E-03 0.2415693 at 90iterations 3.6253615E-03 0.1163731 at 100iterations 1.6678820E-03 4.9533844E-02 at 110iterations 7.6404342E-04 2.3700714E-02 at 120iterations finished qdiffx linear iterations at : 21:08:38 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 7.6404342E-04 2.3700714E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.980000 DelPhi exited at 21:08:38 6.986u 0.179s 0:07.50 95.3% 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 21:08:38 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 = 2606 !!! 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 595 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.784053 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): -32.12600 17.37300 ymin,ymax (A): -23.81100 23.20100 zmin,zma (A): -12.51100 45.03100 x,y,z range (A): 49.49900 47.01200 57.54200 scale (grids/A): 2.784053 object centre (A): -7.376500 -0.3049994 16.26000 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 84.18108 85.91886 88.29406 assigned negative charge : -388.8955 centred at (gu) : 83.64495 86.13357 87.82468 start vw surface at 0.1800000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 164601 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21600 grid for indexing accessible points = 1.400000 m= 81630 mr = 120722 m= 27180 mr = 67581 m= 5793 mr = 21675 m= 642 mr = 4304 m= 44 mr = 418 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 17538 time to turn everything in is 1.230000 number of dielectric boundary points 65174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 19723 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) : 1.856035 object centre at (A) : -7.376500 -0.3049994 16.26000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1855183E-02 0.1999989 midg,1,midg; midg,igrid,midg 0.1657371 5.5278558E-02 1,midg,midg; igrid,midg,midg -6.8355136E-02 0.4947668 gauss-seidel spectral radius is 0.9992324 estimated iterations to convergence 285 setup time was (sec) 1.500000 now iterating at: 21:08:40 rms-change max change #iterations 9.446684 339.1151 at 10iterations 5.426489 133.9662 at 20iterations 3.097872 66.13617 at 30iterations 1.766782 38.95305 at 40iterations 1.010686 19.30984 at 50iterations 0.5727053 11.86079 at 60iterations 0.3269585 6.515826 at 70iterations 0.1853923 3.750347 at 80iterations 0.1056485 2.019352 at 90iterations 6.0120057E-02 1.233999 at 100iterations 3.4198325E-02 0.6261363 at 110iterations 1.9457068E-02 0.3575573 at 120iterations 1.1054887E-02 0.2187302 at 130iterations 6.2855291E-03 0.1209984 at 140iterations 3.5711371E-03 6.3838959E-02 at 150iterations 2.0290616E-03 3.7277222E-02 at 160iterations 1.1562136E-03 2.0875931E-02 at 170iterations 6.5919600E-04 1.2541294E-02 at 180iterations finished qdiffx linear iterations at : 21:08:50 total time elapsed so far: 11.14000 # loops : 180 mean,max change (kT/e) : 6.5919600E-04 1.2541294E-02 energy calculations done at 11.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.38000 DelPhi exited at 21:08:50 11.378u 0.192s 0:11.84 97.6% 0+0k 0+0io 0pf+0w