Wed Feb 15 08:57:43 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:57:43 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 ! Automatically converted by prot2crg.py # of charge parameter records: 339 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3229 !!! WARNING: NAP 528 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5227300 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): 20.49900 88.60300 ymin,ymax (A): -7.472000 48.14600 zmin,zma (A): 23.49000 74.36800 x,y,z range (A): 68.10400 55.61800 50.87801 scale (grids/A): 0.5227300 object centre (A): 54.55100 20.33700 48.92900 number of atom coordinates read : 3229 total number of charged atoms : 3091 net assigned charge : 5.000031 assigned positive charge : 482.4337 centred at (gu) : 88.72520 90.59366 90.22685 assigned negative charge : -477.4351 centred at (gu) : 88.62843 90.63747 90.18795 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5688 nv = 96 ne = 84 npr = 66843 no. pairs analyzed = 66843 no. exposed pairs = 4019 no. arc points = 28265 no. surface atoms = 1344 nbur = 1885 mkacc time = 0.1500000 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 = 1.624000 m= 209 mr = 2938 m= 0 mr = 10 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 2949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2816 ## 378 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7550 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2208222E-11 2.5018959E-10 midg,1,midg; midg,igrid,midg 2.1484511E-10 -2.8862845E-12 1,midg,midg; igrid,midg,midg -2.2177156E-10 2.8797609E-10 gauss-seidel spectral radius is 0.9811686 estimated iterations to convergence 60 setup time was (sec) 0.5900000 now iterating at: 08:57:44 rms-change max change #iterations 5.9371807E-02 12.19263 at 10iterations 3.6029934E-03 0.6660266 at 20iterations 2.7130271E-04 4.3024063E-02 at 30iterations 3.6049434E-05 5.0468445E-03 at 40iterations 6.8152813E-06 9.5558167E-04 at 50iterations finished qdiffx linear iterations at : 08:57:46 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 6.8152813E-06 9.5558167E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 08:57:47 3.422u 0.149s 0:04.03 88.3% 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 Wed Feb 15 2012 at 08:57:47 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 ! Automatically converted by prot2crg.py # of charge parameter records: 339 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3229 !!! WARNING: NAP 528 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.568190 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): 20.49900 88.60300 ymin,ymax (A): -7.472000 48.14600 zmin,zma (A): 23.49000 74.36800 x,y,z range (A): 68.10400 55.61800 50.87801 scale (grids/A): 1.568190 object centre (A): 54.55100 20.33700 48.92900 number of atom coordinates read : 3229 total number of charged atoms : 3091 net assigned charge : 5.000031 assigned positive charge : 482.4337 centred at (gu) : 86.17487 91.78003 90.67969 assigned negative charge : -477.4351 centred at (gu) : 85.88507 91.91201 90.56349 start vw surface at 0.1900000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 64180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28265 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18517 mr = 43960 m= 1620 mr = 12274 m= 42 mr = 688 m= 0 mr = 4 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 806 time to turn everything in is 0.5800000 number of dielectric boundary points 27433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 328 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 23424 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) : 0.5227300 object centre at (A) : 54.55100 20.33700 48.92900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9837292E-03 7.8688730E-03 midg,1,midg; midg,igrid,midg 5.3525497E-03 2.2132937E-03 1,midg,midg; igrid,midg,midg -1.1620039E-02 6.1484566E-03 gauss-seidel spectral radius is 0.9980526 estimated iterations to convergence 180 setup time was (sec) 0.8800000 now iterating at: 08:57:48 rms-change max change #iterations 3.171376 142.3480 at 10iterations 1.286593 48.83630 at 20iterations 0.5198912 19.72705 at 30iterations 0.2102398 8.033024 at 40iterations 8.4821306E-02 3.545089 at 50iterations 3.4247365E-02 1.381193 at 60iterations 1.3894418E-02 0.4916000 at 70iterations 5.6406176E-03 0.2069635 at 80iterations 2.2864046E-03 8.4074259E-02 at 90iterations 9.2606869E-04 3.5557985E-02 at 100iterations 3.7857532E-04 1.4097214E-02 at 110iterations 1.5544344E-04 6.5612793E-03 at 120iterations finished qdiffx linear iterations at : 08:57:55 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 1.5544344E-04 6.5612793E-03 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 08:57:55 7.620u 0.208s 0:08.17 95.7% 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 Wed Feb 15 2012 at 08:57:55 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 ! Automatically converted by prot2crg.py # of charge parameter records: 339 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3229 !!! WARNING: NAP 528 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.352285 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): 20.49900 88.60300 ymin,ymax (A): -7.472000 48.14600 zmin,zma (A): 23.49000 74.36800 x,y,z range (A): 68.10400 55.61800 50.87801 scale (grids/A): 2.352285 object centre (A): 54.55100 20.33700 48.92900 number of atom coordinates read : 3229 total number of charged atoms : 3091 net assigned charge : 5.000031 assigned positive charge : 482.4337 centred at (gu) : 84.26215 92.66978 91.01948 assigned negative charge : -477.4351 centred at (gu) : 83.82745 92.86794 90.84514 start vw surface at 0.1800000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 149466 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28265 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 66438 mr = 108099 m= 16885 mr = 51809 m= 2383 mr = 12031 m= 174 mr = 1445 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 2936 time to turn everything in is 1.140000 number of dielectric boundary points 61896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 24680 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) : 1.568190 object centre at (A) : 54.55100 20.33700 48.92900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1005980E-02 0.1422397 midg,1,midg; midg,igrid,midg 7.6142453E-02 2.0044412E-02 1,midg,midg; igrid,midg,midg -0.3120313 5.2796986E-02 gauss-seidel spectral radius is 0.9991031 estimated iterations to convergence 264 setup time was (sec) 1.430000 now iterating at: 08:57:57 rms-change max change #iterations 8.399743 263.6630 at 10iterations 4.693671 136.7346 at 20iterations 2.602064 65.13907 at 30iterations 1.435656 32.85815 at 40iterations 0.7883329 17.92120 at 50iterations 0.4324110 10.04832 at 60iterations 0.2363860 6.035626 at 70iterations 0.1292031 2.730105 at 80iterations 7.0487536E-02 1.521885 at 90iterations 3.8385853E-02 0.9311275 at 100iterations 2.0919921E-02 0.4659982 at 110iterations 1.1368388E-02 0.2576294 at 120iterations 6.1819647E-03 0.1414585 at 130iterations 3.3652892E-03 7.0760727E-02 at 140iterations 1.8282920E-03 4.0478706E-02 at 150iterations 9.9231582E-04 2.1911621E-02 at 160iterations 5.4152665E-04 1.2465477E-02 at 170iterations 2.9390142E-04 6.3381195E-03 at 180iterations finished qdiffx linear iterations at : 08:58:07 total time elapsed so far: 11.39000 # loops : 180 mean,max change (kT/e) : 2.9390142E-04 6.3381195E-03 energy calculations done at 11.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.57000 DelPhi exited at 08:58:08 11.575u 0.169s 0:12.35 94.9% 0+0k 0+0io 0pf+0w