Tue Oct 11 03:44:06 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 Tue Oct 11 2011 at 03:44:06 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3222 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6069803 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): -12.25700 37.18200 ymin,ymax (A): -27.23300 21.39800 zmin,zma (A): -13.20500 45.44600 x,y,z range (A): 49.43900 48.63100 58.65100 scale (grids/A): 0.6069803 object centre (A): 12.46250 -2.917500 16.12050 number of atom coordinates read : 3222 total number of charged atoms : 2803 net assigned charge : -1.859980 assigned positive charge : 448.6432 centred at (gu) : 90.20451 91.01668 92.35668 assigned negative charge : -450.5041 centred at (gu) : 89.96175 90.94038 92.24408 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7117 nv = 96 ne = 84 npr = 60940 no. pairs analyzed = 60940 no. exposed pairs = 3448 no. arc points = 24009 no. surface atoms = 1165 nbur = 2057 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 344 mr = 4069 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.3500000 number of dielectric boundary points 3367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2483 ## 287 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8950 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2106953E-09 7.9867180E-09 midg,1,midg; midg,igrid,midg -4.1417771E-09 3.4810004E-09 1,midg,midg; igrid,midg,midg -1.3556860E-08 1.1640139E-08 gauss-seidel spectral radius is 0.9859713 estimated iterations to convergence 69 setup time was (sec) 0.6500000 now iterating at: 03:44:07 rms-change max change #iterations 0.1196967 17.39857 at 10iterations 1.0817145E-02 1.365151 at 20iterations 1.0542175E-03 0.1448135 at 30iterations 1.6751626E-04 1.9828796E-02 at 40iterations 4.4630713E-05 5.8765411E-03 at 50iterations finished qdiffx linear iterations at : 03:44:11 total time elapsed so far: 4.510000 # loops : 50 mean,max change (kT/e) : 4.4630713E-05 5.8765411E-03 energy calculations done at 4.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.680000 DelPhi exited at 03:44:12 4.682u 0.397s 0:05.74 88.3% 0+0k 0+0io 6pf+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 03:44:12 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3222 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.820941 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): -12.25700 37.18200 ymin,ymax (A): -27.23300 21.39800 zmin,zma (A): -13.20500 45.44600 x,y,z range (A): 49.43900 48.63100 58.65100 scale (grids/A): 1.820941 object centre (A): 12.46250 -2.917500 16.12050 number of atom coordinates read : 3222 total number of charged atoms : 2803 net assigned charge : -1.859980 assigned positive charge : 448.6432 centred at (gu) : 90.61256 93.04945 97.06908 assigned negative charge : -450.5041 centred at (gu) : 89.88483 92.82098 96.73187 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 77492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24009 grid for indexing accessible points = 1.400000 m= 27609 mr = 55053 m= 3819 mr = 20717 m= 174 mr = 2254 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 2761 time to turn everything in is 0.6400000 number of dielectric boundary points 31032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 197 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 21844 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) : 0.6069803 object centre at (A) : 12.46250 -2.917500 16.12050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5825852E-02 -2.2501121E-03 midg,1,midg; midg,igrid,midg -8.9713000E-03 -2.0040057E-03 1,midg,midg; igrid,midg,midg -9.0100095E-03 3.7773039E-02 gauss-seidel spectral radius is 0.9985376 estimated iterations to convergence 207 setup time was (sec) 1.000000 now iterating at: 03:44:14 rms-change max change #iterations 4.223081 193.8565 at 10iterations 1.933340 63.52466 at 20iterations 0.8788339 28.07450 at 30iterations 0.4031351 13.50021 at 40iterations 0.1841574 5.835485 at 50iterations 8.4088914E-02 2.521895 at 60iterations 3.8577460E-02 1.143310 at 70iterations 1.7561382E-02 0.5510767 at 80iterations 8.0534043E-03 0.2919960 at 90iterations 3.6841999E-03 0.1172791 at 100iterations 1.6826597E-03 5.9114456E-02 at 110iterations 7.6887605E-04 2.6290894E-02 at 120iterations finished qdiffx linear iterations at : 03:44:24 total time elapsed so far: 11.83000 # loops : 120 mean,max change (kT/e) : 7.6887605E-04 2.6290894E-02 energy calculations done at 11.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.00000 DelPhi exited at 03:44:25 12.006u 0.434s 0:13.19 94.2% 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 03:44:25 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3222 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.731411 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): -12.25700 37.18200 ymin,ymax (A): -27.23300 21.39800 zmin,zma (A): -13.20500 45.44600 x,y,z range (A): 49.43900 48.63100 58.65100 scale (grids/A): 2.731411 object centre (A): 12.46250 -2.917500 16.12050 number of atom coordinates read : 3222 total number of charged atoms : 2803 net assigned charge : -1.859980 assigned positive charge : 448.6432 centred at (gu) : 90.91870 94.57406 100.6036 assigned negative charge : -450.5041 centred at (gu) : 89.82716 94.23135 100.0976 start vw surface at 0.1400000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 179549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24009 grid for indexing accessible points = 1.400000 m= 91243 mr = 133400 m= 31154 mr = 75664 m= 6568 mr = 25070 m= 789 mr = 4712 m= 29 mr = 495 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 9151 time to turn everything in is 1.630000 number of dielectric boundary points 69986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 22422 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) : 1.820941 object centre at (A) : 12.46250 -2.917500 16.12050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9804723 0.1476412 midg,1,midg; midg,igrid,midg -0.1220586 -7.7125013E-02 1,midg,midg; igrid,midg,midg -8.5416965E-02 0.3668691 gauss-seidel spectral radius is 0.9992306 estimated iterations to convergence 285 setup time was (sec) 1.960000 now iterating at: 03:44:28 rms-change max change #iterations 10.03703 326.8911 at 10iterations 5.796273 151.7766 at 20iterations 3.332991 73.97651 at 30iterations 1.910530 41.84275 at 40iterations 1.092378 29.05910 at 50iterations 0.6247228 11.37008 at 60iterations 0.3564871 6.580497 at 70iterations 0.2036937 3.884347 at 80iterations 0.1160172 2.225836 at 90iterations 6.6089764E-02 1.141081 at 100iterations 3.7770703E-02 0.6849542 at 110iterations 2.1541577E-02 0.4030285 at 120iterations 1.2295415E-02 0.2221756 at 130iterations 7.0053041E-03 0.1287742 at 140iterations 4.0182080E-03 7.9444885E-02 at 150iterations 2.3190707E-03 4.3789595E-02 at 160iterations 1.3524317E-03 2.4612427E-02 at 170iterations 8.0338493E-04 1.5271187E-02 at 180iterations finished qdiffx linear iterations at : 03:44:47 total time elapsed so far: 20.45000 # loops : 180 mean,max change (kT/e) : 8.0338493E-04 1.5271187E-02 energy calculations done at 20.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.62000 DelPhi exited at 03:44:47 20.624u 0.495s 0:21.94 96.2% 0+0k 0+0io 0pf+0w