Sun Oct 9 09:41:19 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 Sun Oct 9 2011 at 09:41:19 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 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: 0.6056894 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): -7.748000 48.80300 ymin,ymax (A): 15.63400 67.14400 zmin,zma (A): 62.16400 120.9400 x,y,z range (A): 56.55100 51.51000 58.77600 scale (grids/A): 0.6056894 object centre (A): 20.52750 41.38900 91.55200 number of atom coordinates read : 2579 total number of charged atoms : 2438 net assigned charge : 7.000014 assigned positive charge : 380.9390 centred at (gu) : 89.03868 90.23227 89.46004 assigned negative charge : -373.9395 centred at (gu) : 89.09930 90.32491 89.39837 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6477 nv = 96 ne = 84 npr = 51397 no. pairs analyzed = 51397 no. exposed pairs = 3346 no. arc points = 23919 no. surface atoms = 1118 nbur = 1461 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 3393 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2475 ## 262 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7937 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1100251E-09 5.4680518E-09 midg,1,midg; midg,igrid,midg 7.0604727E-09 -3.4294895E-10 1,midg,midg; igrid,midg,midg 7.5885680E-09 8.7443108E-10 gauss-seidel spectral radius is 0.9858975 estimated iterations to convergence 69 setup time was (sec) 0.3800000 now iterating at: 09:41:19 rms-change max change #iterations 0.1149251 17.58684 at 10iterations 9.8974453E-03 1.759318 at 20iterations 8.5824134E-04 0.1388960 at 30iterations 7.4082091E-05 1.0860443E-02 at 40iterations 6.6224279E-06 9.6893311E-04 at 50iterations finished qdiffx linear iterations at : 09:41:22 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 6.6224279E-06 9.6893311E-04 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 09:41:23 3.384u 0.190s 0:03.85 92.7% 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 Sun Oct 9 2011 at 09:41:23 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 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: 1.817068 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): -7.748000 48.80300 ymin,ymax (A): 15.63400 67.14400 zmin,zma (A): 62.16400 120.9400 x,y,z range (A): 56.55100 51.51000 58.77600 scale (grids/A): 1.817068 object centre (A): 20.52750 41.38900 91.55200 number of atom coordinates read : 2579 total number of charged atoms : 2438 net assigned charge : 7.000014 assigned positive charge : 380.9390 centred at (gu) : 87.11574 90.69636 88.37958 assigned negative charge : -373.9395 centred at (gu) : 87.29764 90.97450 88.19473 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 69850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23919 grid for indexing accessible points = 1.400000 m= 24209 mr = 46976 m= 3448 mr = 17328 m= 169 mr = 1927 m= 0 mr = 57 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 187 time to turn everything in is 0.3400000 number of dielectric boundary points 31388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 218 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19077 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) : 0.6056894 object centre at (A) : 20.52750 41.38900 91.55200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1863937E-02 1.8817885E-02 midg,1,midg; midg,igrid,midg 3.3250142E-02 7.9514552E-03 1,midg,midg; igrid,midg,midg 2.0219968E-03 -3.6354945E-03 gauss-seidel spectral radius is 0.9985136 estimated iterations to convergence 206 setup time was (sec) 0.5600000 now iterating at: 09:41:24 rms-change max change #iterations 3.821083 200.8958 at 10iterations 1.725117 62.10987 at 20iterations 0.7803429 27.38932 at 30iterations 0.3536424 12.44194 at 40iterations 0.1591898 5.348195 at 50iterations 7.2127573E-02 2.341995 at 60iterations 3.2825924E-02 1.111381 at 70iterations 1.4771360E-02 0.4736781 at 80iterations 6.7403722E-03 0.2283669 at 90iterations 3.0426411E-03 0.1040421 at 100iterations 1.3814622E-03 4.5083284E-02 at 110iterations 6.2430638E-04 2.1922112E-02 at 120iterations finished qdiffx linear iterations at : 09:41:31 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 6.2430638E-04 2.1922112E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 09:41:31 7.805u 0.217s 0:08.37 95.6% 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 Sun Oct 9 2011 at 09:41:31 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 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: 2.725602 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): -7.748000 48.80300 ymin,ymax (A): 15.63400 67.14400 zmin,zma (A): 62.16400 120.9400 x,y,z range (A): 56.55100 51.51000 58.77600 scale (grids/A): 2.725602 object centre (A): 20.52750 41.38900 91.55200 number of atom coordinates read : 2579 total number of charged atoms : 2438 net assigned charge : 7.000014 assigned positive charge : 380.9390 centred at (gu) : 85.67352 91.04446 87.56931 assigned negative charge : -373.9395 centred at (gu) : 85.94642 91.46171 87.29197 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 161895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23919 grid for indexing accessible points = 1.400000 m= 79418 mr = 114791 m= 27552 mr = 63821 m= 5873 mr = 21614 m= 785 mr = 4070 m= 37 mr = 474 m= 0 mr = 12 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 615 time to turn everything in is 0.8800000 number of dielectric boundary points 70778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 19496 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) : 1.817068 object centre at (A) : 20.52750 41.38900 91.55200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4013282 6.4455271E-02 midg,1,midg; midg,igrid,midg 0.3442660 8.5810214E-02 1,midg,midg; igrid,midg,midg -5.7082489E-02 -0.1133002 gauss-seidel spectral radius is 0.9992308 estimated iterations to convergence 285 setup time was (sec) 1.120000 now iterating at: 09:41:32 rms-change max change #iterations 9.283658 282.6170 at 10iterations 5.432324 145.3553 at 20iterations 3.154178 74.56065 at 30iterations 1.812159 37.37880 at 40iterations 1.037120 20.37359 at 50iterations 0.5966937 13.87678 at 60iterations 0.3415954 7.331407 at 70iterations 0.1946582 4.582119 at 80iterations 0.1111194 2.159088 at 90iterations 6.3329205E-02 1.262199 at 100iterations 3.5989575E-02 0.7052689 at 110iterations 2.0487942E-02 0.4090271 at 120iterations 1.1656516E-02 0.2642217 at 130iterations 6.6316966E-03 0.1292114 at 140iterations 3.7618023E-03 7.7592850E-02 at 150iterations 2.1380042E-03 3.9020538E-02 at 160iterations 1.2177879E-03 2.2763968E-02 at 170iterations 6.9088856E-04 1.4090776E-02 at 180iterations finished qdiffx linear iterations at : 09:41:44 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 6.9088856E-04 1.4090776E-02 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 09:41:44 12.552u 0.238s 0:13.12 97.4% 0+0k 0+0io 0pf+0w