Mon Oct 10 14:00:41 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 Mon Oct 10 2011 at 14:00:41 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3101 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: 0.5548196 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): -9.530000 48.15900 ymin,ymax (A): -19.25300 29.61100 zmin,zma (A): -22.72800 41.43700 x,y,z range (A): 57.68900 48.86400 64.16500 scale (grids/A): 0.5548196 object centre (A): 19.31450 5.179000 9.354500 number of atom coordinates read : 3101 total number of charged atoms : 2966 net assigned charge : 3.500005 assigned positive charge : 472.7679 centred at (gu) : 88.32365 89.12132 90.63668 assigned negative charge : -469.2690 centred at (gu) : 88.24567 89.11787 90.50874 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6344 nv = 96 ne = 84 npr = 61842 no. pairs analyzed = 61842 no. exposed pairs = 4140 no. arc points = 28833 no. surface atoms = 1373 nbur = 1728 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 268 mr = 3224 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3381 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2952 ## 368 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8157 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.0510149E-10 1.7891392E-09 midg,1,midg; midg,igrid,midg 3.4267497E-10 2.8040897E-10 1,midg,midg; igrid,midg,midg -6.9375533E-10 7.0518935E-10 gauss-seidel spectral radius is 0.9832603 estimated iterations to convergence 64 setup time was (sec) 0.4300000 now iterating at: 14:00:41 rms-change max change #iterations 8.2349114E-02 14.43501 at 10iterations 5.9090476E-03 0.9996796 at 20iterations 4.9359084E-04 7.7857971E-02 at 30iterations 5.9059472E-05 1.0807037E-02 at 40iterations 9.7823395E-06 1.7051697E-03 at 50iterations finished qdiffx linear iterations at : 14:00:44 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 9.7823395E-06 1.7051697E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 14:00:45 3.455u 0.163s 0:04.01 90.0% 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 Mon Oct 10 2011 at 14:00:45 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3101 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: 1.664459 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): -9.530000 48.15900 ymin,ymax (A): -19.25300 29.61100 zmin,zma (A): -22.72800 41.43700 x,y,z range (A): 57.68900 48.86400 64.16500 scale (grids/A): 1.664459 object centre (A): 19.31450 5.179000 9.354500 number of atom coordinates read : 3101 total number of charged atoms : 2966 net assigned charge : 3.500005 assigned positive charge : 472.7679 centred at (gu) : 84.97025 87.36302 91.90900 assigned negative charge : -469.2690 centred at (gu) : 84.73660 87.35352 91.52625 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69915 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28833 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 21880 mr = 47115 m= 2512 mr = 14619 m= 70 mr = 1237 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 563 time to turn everything in is 0.3500000 number of dielectric boundary points 31403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 285 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 22835 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) : 0.5548196 object centre at (A) : 19.31450 5.179000 9.354500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7199231E-03 2.7315784E-02 midg,1,midg; midg,igrid,midg 7.7473937E-04 2.3430372E-03 1,midg,midg; igrid,midg,midg -7.5351689E-03 9.1392879E-04 gauss-seidel spectral radius is 0.9982741 estimated iterations to convergence 191 setup time was (sec) 0.5700000 now iterating at: 14:00:46 rms-change max change #iterations 3.569266 163.3474 at 10iterations 1.522313 57.06681 at 20iterations 0.6477309 25.91113 at 30iterations 0.2758055 9.799957 at 40iterations 0.1178205 3.989048 at 50iterations 5.0363757E-02 1.781886 at 60iterations 2.1368993E-02 0.7836788 at 70iterations 9.1173667E-03 0.3322010 at 80iterations 3.9267028E-03 0.1463952 at 90iterations 1.6892920E-03 5.9546471E-02 at 100iterations 7.3356979E-04 2.6100159E-02 at 110iterations 3.2271730E-04 1.0898590E-02 at 120iterations finished qdiffx linear iterations at : 14:00:53 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 3.2271730E-04 1.0898590E-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 14:00:53 7.804u 0.218s 0:08.53 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 Mon Oct 10 2011 at 14:00:53 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3101 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: 2.496688 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): -9.530000 48.15900 ymin,ymax (A): -19.25300 29.61100 zmin,zma (A): -22.72800 41.43700 x,y,z range (A): 57.68900 48.86400 64.16500 scale (grids/A): 2.496688 object centre (A): 19.31450 5.179000 9.354500 number of atom coordinates read : 3101 total number of charged atoms : 2966 net assigned charge : 3.500005 assigned positive charge : 472.7679 centred at (gu) : 82.45499 86.04435 92.86338 assigned negative charge : -469.2690 centred at (gu) : 82.10480 86.03010 92.28929 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 162575 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28833 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 74884 mr = 115640 m= 21844 mr = 58520 m= 4097 mr = 15937 m= 322 mr = 2704 m= 6 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 2069 time to turn everything in is 0.8600000 number of dielectric boundary points 70803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 23703 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) : 1.664459 object centre at (A) : 19.31450 5.179000 9.354500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1458044 0.4390851 midg,1,midg; midg,igrid,midg -2.0715179E-02 3.1968836E-02 1,midg,midg; igrid,midg,midg -9.0596572E-02 -1.1401701E-02 gauss-seidel spectral radius is 0.9991695 estimated iterations to convergence 274 setup time was (sec) 1.100000 now iterating at: 14:00:55 rms-change max change #iterations 9.208232 297.6436 at 10iterations 5.232993 128.2301 at 20iterations 2.948281 67.21052 at 30iterations 1.657944 34.35259 at 40iterations 0.9273627 20.01564 at 50iterations 0.5190763 11.13759 at 60iterations 0.2899120 6.069424 at 70iterations 0.1615784 3.232758 at 80iterations 8.9970119E-02 1.847610 at 90iterations 5.0058819E-02 0.9716541 at 100iterations 2.7915385E-02 0.5646915 at 110iterations 1.5544068E-02 0.3021660 at 120iterations 8.6372541E-03 0.1854377 at 130iterations 4.8083048E-03 0.1035480 at 140iterations 2.6794963E-03 5.7046890E-02 at 150iterations 1.4931401E-03 3.0063629E-02 at 160iterations 8.3585276E-04 1.6872406E-02 at 170iterations 4.6951420E-04 9.5233917E-03 at 180iterations finished qdiffx linear iterations at : 14:01:06 total time elapsed so far: 12.21000 # loops : 180 mean,max change (kT/e) : 4.6951420E-04 9.5233917E-03 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.35000 DelPhi exited at 14:01:07 12.348u 0.214s 0:13.57 92.4% 0+0k 0+0io 0pf+0w