Tue Oct 11 03:26:10 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 Tue Oct 11 2011 at 03:26:10 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2473 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6075500 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): -19.56500 26.44200 ymin,ymax (A): -16.90900 41.68700 zmin,zma (A): -24.75500 25.16500 x,y,z range (A): 46.00700 58.59600 49.92000 scale (grids/A): 0.6075500 object centre (A): 3.438499 12.38900 0.2050009 number of atom coordinates read : 2473 total number of charged atoms : 2324 net assigned charge : 5.9306622E-06 assigned positive charge : 362.0560 centred at (gu) : 90.85757 90.51743 88.88411 assigned negative charge : -362.0567 centred at (gu) : 90.88460 90.68115 89.06967 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6307 nv = 96 ne = 84 npr = 48205 no. pairs analyzed = 48205 no. exposed pairs = 3554 no. arc points = 25759 no. surface atoms = 1172 nbur = 1301 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 3007 m= 0 mr = 16 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.2700000 number of dielectric boundary points 3585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2519 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7637 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0011173E-08 -6.3218337E-09 midg,1,midg; midg,igrid,midg 6.0849596E-09 -8.0803302E-09 1,midg,midg; igrid,midg,midg 9.2152452E-10 -1.4538437E-09 gauss-seidel spectral radius is 0.9859812 estimated iterations to convergence 69 setup time was (sec) 0.5200000 now iterating at: 03:26:11 rms-change max change #iterations 0.1146893 18.70285 at 10iterations 9.6486956E-03 1.547025 at 20iterations 8.4073358E-04 0.1383324 at 30iterations 7.4782212E-05 1.4987946E-02 at 40iterations 6.5229083E-06 1.1559725E-03 at 50iterations finished qdiffx linear iterations at : 03:26:14 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 6.5229083E-06 1.1559725E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 03:26:14 3.380u 0.178s 0:04.06 87.4% 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 Tue Oct 11 2011 at 03:26:14 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2473 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: 1.822650 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): -19.56500 26.44200 ymin,ymax (A): -16.90900 41.68700 zmin,zma (A): -24.75500 25.16500 x,y,z range (A): 46.00700 58.59600 49.92000 scale (grids/A): 1.822650 object centre (A): 3.438499 12.38900 0.2050009 number of atom coordinates read : 2473 total number of charged atoms : 2324 net assigned charge : 5.9306622E-06 assigned positive charge : 362.0560 centred at (gu) : 92.57198 91.55162 86.65195 assigned negative charge : -362.0567 centred at (gu) : 92.65379 92.04313 87.20876 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 67956 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25759 grid for indexing accessible points = 1.400000 m= 21366 mr = 43371 m= 2605 mr = 14130 m= 90 mr = 1174 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 699 time to turn everything in is 0.4900000 number of dielectric boundary points 33327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 205 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 18216 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) : 0.6075500 object centre at (A) : 3.438499 12.38900 0.2050009 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7651349E-02 -1.7116120E-02 midg,1,midg; midg,igrid,midg 7.2657098E-03 -1.6206715E-02 1,midg,midg; igrid,midg,midg 4.7293711E-03 2.5597399E-03 gauss-seidel spectral radius is 0.9985209 estimated iterations to convergence 206 setup time was (sec) 0.7900000 now iterating at: 03:26:15 rms-change max change #iterations 3.754152 184.9061 at 10iterations 1.694585 60.50858 at 20iterations 0.7651102 28.01438 at 30iterations 0.3468459 15.13767 at 40iterations 0.1568425 5.052795 at 50iterations 7.1057647E-02 2.359192 at 60iterations 3.2369047E-02 1.086235 at 70iterations 1.4641258E-02 0.4932938 at 80iterations 6.6515170E-03 0.2303085 at 90iterations 3.0107016E-03 0.1140509 at 100iterations 1.3648494E-03 4.9326897E-02 at 110iterations 6.1969360E-04 2.4017334E-02 at 120iterations finished qdiffx linear iterations at : 03:26:22 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 6.1969360E-04 2.4017334E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 03:26:23 7.674u 0.242s 0:08.22 96.2% 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 Tue Oct 11 2011 at 03:26:23 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2473 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.733975 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): -19.56500 26.44200 ymin,ymax (A): -16.90900 41.68700 zmin,zma (A): -24.75500 25.16500 x,y,z range (A): 46.00700 58.59600 49.92000 scale (grids/A): 2.733975 object centre (A): 3.438499 12.38900 0.2050009 number of atom coordinates read : 2473 total number of charged atoms : 2324 net assigned charge : 5.9306622E-06 assigned positive charge : 362.0560 centred at (gu) : 93.85785 92.32726 84.97787 assigned negative charge : -362.0567 centred at (gu) : 93.98048 93.06468 85.81311 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 157273 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25759 grid for indexing accessible points = 1.400000 m= 71665 mr = 106612 m= 22258 mr = 55215 m= 4138 mr = 16073 m= 398 mr = 2546 m= 14 mr = 167 m= 0 mr = 5 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 2408 time to turn everything in is 1.190000 number of dielectric boundary points 75128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 18581 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) : 1.822650 object centre at (A) : 3.438499 12.38900 0.2050009 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1819835 -0.1651978 midg,1,midg; midg,igrid,midg 2.7544808E-02 0.1943476 1,midg,midg; igrid,midg,midg 4.5162767E-02 1.3306966E-02 gauss-seidel spectral radius is 0.9992373 estimated iterations to convergence 286 setup time was (sec) 1.510000 now iterating at: 03:26:24 rms-change max change #iterations 9.104011 271.3552 at 10iterations 5.327373 130.7968 at 20iterations 3.082524 69.30884 at 30iterations 1.779079 39.12454 at 40iterations 1.021416 23.63142 at 50iterations 0.5855340 12.88882 at 60iterations 0.3358955 6.962147 at 70iterations 0.1922617 3.961708 at 80iterations 0.1098847 2.431695 at 90iterations 6.2653229E-02 1.200932 at 100iterations 3.5723947E-02 0.6924438 at 110iterations 2.0326201E-02 0.4110489 at 120iterations 1.1620246E-02 0.2302399 at 130iterations 6.6344254E-03 0.1310883 at 140iterations 3.7707614E-03 7.5784683E-02 at 150iterations 2.1464988E-03 4.3983459E-02 at 160iterations 1.2204263E-03 2.2865295E-02 at 170iterations 6.9600338E-04 1.3998389E-02 at 180iterations finished qdiffx linear iterations at : 03:26:35 total time elapsed so far: 12.21000 # loops : 180 mean,max change (kT/e) : 6.9600338E-04 1.3998389E-02 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 03:26:36 12.383u 0.260s 0:13.09 96.5% 0+0k 0+0io 0pf+0w