Sun Oct 9 23:21:11 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 23:21:11 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2285 !!! WARNING: SEP 217 has a net charge of -0.4750 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: 0.6663173 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): -11.94300 32.94000 ymin,ymax (A): -22.15300 29.95700 zmin,zma (A): -10.82400 42.60400 x,y,z range (A): 44.88300 52.11000 53.42800 scale (grids/A): 0.6663173 object centre (A): 10.49850 3.901999 15.89000 number of atom coordinates read : 2285 total number of charged atoms : 2143 net assigned charge : 2.5010556E-02 assigned positive charge : 339.3294 centred at (gu) : 91.62493 90.65791 90.58839 assigned negative charge : -339.3048 centred at (gu) : 91.55547 90.58085 90.27919 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6989 nv = 96 ne = 84 npr = 44947 no. pairs analyzed = 44947 no. exposed pairs = 3063 no. arc points = 21359 no. surface atoms = 1023 nbur = 1262 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3733 m= 3 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2800000 number of dielectric boundary points 3619 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2006 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8037 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7699204E-08 6.7971925E-08 midg,1,midg; midg,igrid,midg -1.4219774E-08 1.7111386E-08 1,midg,midg; igrid,midg,midg -1.0515964E-08 1.8892846E-08 gauss-seidel spectral radius is 0.9883035 estimated iterations to convergence 75 setup time was (sec) 0.5600000 now iterating at: 23:21:12 rms-change max change #iterations 0.1611008 21.93239 at 10iterations 1.7565669E-02 2.627287 at 20iterations 1.8812381E-03 0.2827635 at 30iterations 2.2499502E-04 3.1162262E-02 at 40iterations 4.8824728E-05 8.7347627E-03 at 50iterations finished qdiffx linear iterations at : 23:21:17 total time elapsed so far: 4.950000 # loops : 50 mean,max change (kT/e) : 4.8824728E-05 8.7347627E-03 energy calculations done at 4.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.130000 DelPhi exited at 23:21:17 5.133u 0.459s 0:05.94 93.9% 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 Sun Oct 9 2011 at 23:21:17 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2285 !!! WARNING: SEP 217 has a net charge of -0.4750 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: 1.998952 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): -11.94300 32.94000 ymin,ymax (A): -22.15300 29.95700 zmin,zma (A): -10.82400 42.60400 x,y,z range (A): 44.88300 52.11000 53.42800 scale (grids/A): 1.998952 object centre (A): 10.49850 3.901999 15.89000 number of atom coordinates read : 2285 total number of charged atoms : 2143 net assigned charge : 2.5010556E-02 assigned positive charge : 339.3294 centred at (gu) : 94.87466 91.97339 91.76500 assigned negative charge : -339.3048 centred at (gu) : 94.66632 91.74245 90.83778 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 75202 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21359 grid for indexing accessible points = 1.400000 m= 26656 mr = 51099 m= 4339 mr = 19268 m= 328 mr = 2748 m= 5 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 164 time to turn everything in is 0.6300000 number of dielectric boundary points 33273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 16948 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) : 0.6663173 object centre at (A) : 10.49850 3.901999 15.89000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2594894E-02 8.1495279E-03 midg,1,midg; midg,igrid,midg 2.3491880E-02 2.4998568E-02 1,midg,midg; igrid,midg,midg -1.7546048E-02 2.9923888E-03 gauss-seidel spectral radius is 0.9987334 estimated iterations to convergence 223 setup time was (sec) 0.9800000 now iterating at: 23:21:19 rms-change max change #iterations 4.346583 214.5579 at 10iterations 2.091410 73.54576 at 20iterations 1.004975 32.76666 at 30iterations 0.4844773 18.29854 at 40iterations 0.2329437 7.297399 at 50iterations 0.1124398 3.446066 at 60iterations 5.4325119E-02 1.833435 at 70iterations 2.6165999E-02 0.9059801 at 80iterations 1.2631469E-02 0.3890142 at 90iterations 6.0721058E-03 0.1932664 at 100iterations 2.9339241E-03 9.4776154E-02 at 110iterations 1.4178334E-03 4.6643853E-02 at 120iterations finished qdiffx linear iterations at : 23:21:30 total time elapsed so far: 12.32000 # loops : 120 mean,max change (kT/e) : 1.4178334E-03 4.6643853E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.49000 DelPhi exited at 23:21:31 12.493u 0.517s 0:13.33 97.5% 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 23:21:31 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2285 !!! WARNING: SEP 217 has a net charge of -0.4750 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: 2.998428 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): -11.94300 32.94000 ymin,ymax (A): -22.15300 29.95700 zmin,zma (A): -10.82400 42.60400 x,y,z range (A): 44.88300 52.11000 53.42800 scale (grids/A): 2.998428 object centre (A): 10.49850 3.901999 15.89000 number of atom coordinates read : 2285 total number of charged atoms : 2143 net assigned charge : 2.5010556E-02 assigned positive charge : 339.3294 centred at (gu) : 97.31181 92.96004 92.64742 assigned negative charge : -339.3048 centred at (gu) : 96.99941 92.61370 91.25663 start vw surface at 0.1000000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 173344 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21359 grid for indexing accessible points = 1.400000 m= 86222 mr = 123439 m= 30849 mr = 69680 m= 7947 mr = 24595 m= 1427 mr = 5998 m= 129 mr = 1058 m= 0 mr = 90 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 514 time to turn everything in is 1.660000 number of dielectric boundary points 75058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 17143 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) : 1.998952 object centre at (A) : 10.49850 3.901999 15.89000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7566189 -6.9930896E-02 midg,1,midg; midg,igrid,midg 0.2632990 4.5254577E-02 1,midg,midg; igrid,midg,midg -0.2459449 6.4903520E-02 gauss-seidel spectral radius is 0.9992882 estimated iterations to convergence 296 setup time was (sec) 2.070000 now iterating at: 23:21:33 rms-change max change #iterations 10.08610 327.3980 at 10iterations 5.968559 136.1893 at 20iterations 3.522137 86.17136 at 30iterations 2.067281 42.98403 at 40iterations 1.209512 28.83527 at 50iterations 0.7100731 15.16894 at 60iterations 0.4144887 7.803519 at 70iterations 0.2417741 4.923871 at 80iterations 0.1409660 2.852188 at 90iterations 8.1947275E-02 1.393897 at 100iterations 4.7788329E-02 1.005217 at 110iterations 2.7861796E-02 0.5478392 at 120iterations 1.6184174E-02 0.2988529 at 130iterations 9.4368318E-03 0.1754274 at 140iterations 5.4679466E-03 9.4510198E-02 at 150iterations 3.1769748E-03 5.1940918E-02 at 160iterations 1.8511467E-03 3.3428192E-02 at 170iterations 1.0786245E-03 1.9210815E-02 at 180iterations finished qdiffx linear iterations at : 23:21:53 total time elapsed so far: 21.34000 # loops : 180 mean,max change (kT/e) : 1.0786245E-03 1.9210815E-02 energy calculations done at 21.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.51000 DelPhi exited at 23:21:53 21.512u 0.552s 0:22.39 98.5% 0+0k 0+0io 0pf+0w