Sat Oct 15 14:33:12 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 15 2011 at 14:33:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2839 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: 0.6198635 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): -8.715000 48.71700 ymin,ymax (A): -8.420000 38.74900 zmin,zma (A): -0.2140000 54.41000 x,y,z range (A): 57.43200 47.16900 54.62400 scale (grids/A): 0.6198635 object centre (A): 20.00100 15.16450 27.09800 number of atom coordinates read : 2839 total number of charged atoms : 2698 net assigned charge : -4.999980 assigned positive charge : 424.3552 centred at (gu) : 88.84984 89.76021 89.14261 assigned negative charge : -429.3563 centred at (gu) : 88.80460 89.66712 89.05875 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7373 nv = 96 ne = 84 npr = 57059 no. pairs analyzed = 57059 no. exposed pairs = 3763 no. arc points = 26645 no. surface atoms = 1263 nbur = 1576 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 330 mr = 3810 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.2100000 number of dielectric boundary points 3880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2716 ## 261 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9010 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2161655E-08 1.7810798E-09 midg,1,midg; midg,igrid,midg -1.1333053E-08 2.6982299E-09 1,midg,midg; igrid,midg,midg -9.2656025E-09 -4.9428311E-10 gauss-seidel spectral radius is 0.9865500 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 14:33:13 rms-change max change #iterations 0.1290486 20.71078 at 10iterations 1.2100407E-02 1.800843 at 20iterations 1.0930648E-03 0.1729927 at 30iterations 1.0145144E-04 1.4251351E-02 at 40iterations 9.3051212E-06 1.3973713E-03 at 50iterations finished qdiffx linear iterations at : 14:33:16 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 9.3051212E-06 1.3973713E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 14:33:16 3.527u 0.220s 0:04.28 87.3% 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 15 2011 at 14:33:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2839 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: 1.859590 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): -8.715000 48.71700 ymin,ymax (A): -8.420000 38.74900 zmin,zma (A): -0.2140000 54.41000 x,y,z range (A): 57.43200 47.16900 54.62400 scale (grids/A): 1.859590 object centre (A): 20.00100 15.16450 27.09800 number of atom coordinates read : 2839 total number of charged atoms : 2698 net assigned charge : -4.999980 assigned positive charge : 424.3552 centred at (gu) : 86.54884 89.27966 87.42719 assigned negative charge : -429.3563 centred at (gu) : 86.41341 89.00098 87.17587 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26645 grid for indexing accessible points = 1.400000 m= 26171 mr = 53738 m= 3359 mr = 18217 m= 135 mr = 1750 m= 4 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 577 time to turn everything in is 0.4000000 number of dielectric boundary points 35793 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 234 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 21184 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) : 0.6198635 object centre at (A) : 20.00100 15.16450 27.09800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2262426E-03 5.8710566E-03 midg,1,midg; midg,igrid,midg -2.3002315E-02 -2.6965884E-03 1,midg,midg; igrid,midg,midg -5.3976499E-02 2.5023922E-02 gauss-seidel spectral radius is 0.9986009 estimated iterations to convergence 212 setup time was (sec) 0.6400000 now iterating at: 14:33:17 rms-change max change #iterations 4.236511 199.8020 at 10iterations 1.957821 71.88717 at 20iterations 0.9060227 29.12241 at 30iterations 0.4195941 14.86559 at 40iterations 0.1942413 5.943963 at 50iterations 8.9910068E-02 3.138945 at 60iterations 4.1591268E-02 1.278025 at 70iterations 1.9334204E-02 0.7006073 at 80iterations 8.9544496E-03 0.3117223 at 90iterations 4.1521066E-03 0.1296616 at 100iterations 1.9263963E-03 6.5166473E-02 at 110iterations 8.9252519E-04 2.7495861E-02 at 120iterations finished qdiffx linear iterations at : 14:33:27 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 8.9252519E-04 2.7495861E-02 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.390000 DelPhi exited at 14:33:27 8.389u 0.231s 0:10.92 78.8% 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 Sat Oct 15 2011 at 14:33:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2839 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: 2.789386 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): -8.715000 48.71700 ymin,ymax (A): -8.420000 38.74900 zmin,zma (A): -0.2140000 54.41000 x,y,z range (A): 57.43200 47.16900 54.62400 scale (grids/A): 2.789386 object centre (A): 20.00100 15.16450 27.09800 number of atom coordinates read : 2839 total number of charged atoms : 2698 net assigned charge : -4.999980 assigned positive charge : 424.3552 centred at (gu) : 84.82307 88.91934 86.14072 assigned negative charge : -429.3563 centred at (gu) : 84.62009 88.50141 85.76368 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 184995 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26645 grid for indexing accessible points = 1.400000 m= 87565 mr = 131432 m= 28320 mr = 69554 m= 5655 mr = 21519 m= 539 mr = 3734 m= 17 mr = 253 m= 0 mr = 4 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 1968 time to turn everything in is 1.000000 number of dielectric boundary points 80595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 21581 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) : 1.859590 object centre at (A) : 20.00100 15.16450 27.09800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1552275 -0.2035203 midg,1,midg; midg,igrid,midg -0.2442277 -4.4814542E-02 1,midg,midg; igrid,midg,midg -0.6221133 0.6368524 gauss-seidel spectral radius is 0.9992678 estimated iterations to convergence 292 setup time was (sec) 1.260000 now iterating at: 14:33:29 rms-change max change #iterations 10.28192 318.1708 at 10iterations 6.090576 149.6497 at 20iterations 3.583786 79.97260 at 30iterations 2.098739 47.81719 at 40iterations 1.221388 27.90367 at 50iterations 0.7113941 13.32866 at 60iterations 0.4123149 8.368028 at 70iterations 0.2387620 4.980676 at 80iterations 0.1380696 2.704372 at 90iterations 7.9934530E-02 1.471092 at 100iterations 4.6228774E-02 0.8615661 at 110iterations 2.6627718E-02 0.5677223 at 120iterations 1.5363962E-02 0.2626276 at 130iterations 8.8715451E-03 0.1698227 at 140iterations 5.1202420E-03 0.1023312 at 150iterations 2.9481018E-03 5.7594776E-02 at 160iterations 1.7010103E-03 3.8535118E-02 at 170iterations 9.8015787E-04 1.8680573E-02 at 180iterations finished qdiffx linear iterations at : 14:33:51 total time elapsed so far: 13.41000 # loops : 180 mean,max change (kT/e) : 9.8015787E-04 1.8680573E-02 energy calculations done at 13.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 14:33:52 13.538u 0.254s 0:24.61 55.9% 0+0k 0+0io 0pf+0w