Sat Oct 8 16:32:36 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 Sat Oct 8 2011 at 16:32:36 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: 355 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4549 !!! WARNING: GLM 203 has a net charge of -0.0940 !!! WARNING: FAD 991 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: 0.5378375 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): 17.39100 80.96300 ymin,ymax (A): 118.6600 184.8510 zmin,zma (A): -1.200000 61.08000 x,y,z range (A): 63.57200 66.19099 62.28000 scale (grids/A): 0.5378375 object centre (A): 49.17700 151.7555 29.94000 number of atom coordinates read : 4549 total number of charged atoms : 4359 net assigned charge : 3.906038 assigned positive charge : 696.3897 centred at (gu) : 91.91501 89.42763 87.11916 assigned negative charge : -692.4870 centred at (gu) : 91.88290 89.36411 87.13734 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8469 nv = 96 ne = 84 npr = 89836 no. pairs analyzed = 89836 no. exposed pairs = 6017 no. arc points = 41702 no. surface atoms = 1984 nbur = 2565 mkacc time = 0.2300000 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 = 1.596000 m= 399 mr = 4275 m= 0 mr = 17 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4271 ## 566 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 11242 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2642586E-10 1.7670844E-11 midg,1,midg; midg,igrid,midg -3.6253384E-10 5.5243460E-10 1,midg,midg; igrid,midg,midg -4.3405706E-11 6.5888450E-10 gauss-seidel spectral radius is 0.9823044 estimated iterations to convergence 62 setup time was (sec) 0.7800000 now iterating at: 16:32:37 rms-change max change #iterations 8.5894980E-02 12.86824 at 10iterations 5.8948649E-03 0.9404316 at 20iterations 8.5332285E-04 0.1137385 at 30iterations 2.9531206E-04 4.2889595E-02 at 40iterations 1.1417983E-04 1.6837597E-02 at 50iterations finished qdiffx linear iterations at : 16:32:41 total time elapsed so far: 4.770000 # loops : 50 mean,max change (kT/e) : 1.1417983E-04 1.6837597E-02 energy calculations done at 4.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.930000 DelPhi exited at 16:32:42 4.935u 0.387s 0:05.61 94.6% 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 Sat Oct 8 2011 at 16:32:42 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: 355 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4549 !!! WARNING: GLM 203 has a net charge of -0.0940 !!! WARNING: FAD 991 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.613513 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): 17.39100 80.96300 ymin,ymax (A): 118.6600 184.8510 zmin,zma (A): -1.200000 61.08000 x,y,z range (A): 63.57200 66.19099 62.28000 scale (grids/A): 1.613513 object centre (A): 49.17700 151.7555 29.94000 number of atom coordinates read : 4549 total number of charged atoms : 4359 net assigned charge : 3.906038 assigned positive charge : 696.3897 centred at (gu) : 95.74400 88.28200 81.35654 assigned negative charge : -692.4870 centred at (gu) : 95.64852 88.09214 81.41127 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 92140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41702 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 32198 mr = 61457 m= 4287 mr = 22539 m= 118 mr = 2267 m= 3 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 42476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 456 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 33341 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) : 0.5378375 object centre at (A) : 49.17700 151.7555 29.94000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1428123E-03 6.8700411E-03 midg,1,midg; midg,igrid,midg 1.1299775E-02 2.7588909E-02 1,midg,midg; igrid,midg,midg -8.0545275E-03 -6.4261835E-03 gauss-seidel spectral radius is 0.9982989 estimated iterations to convergence 192 setup time was (sec) 1.110000 now iterating at: 16:32:43 rms-change max change #iterations 4.199234 230.1042 at 10iterations 1.790937 82.11665 at 20iterations 0.7693228 30.54345 at 30iterations 0.3303094 11.66913 at 40iterations 0.1412663 5.498077 at 50iterations 6.0621243E-02 2.214001 at 60iterations 2.6011968E-02 0.8178601 at 70iterations 1.1225642E-02 0.3772175 at 80iterations 4.8617781E-03 0.1543808 at 90iterations 2.1357676E-03 6.6146851E-02 at 100iterations 9.6718199E-04 3.1455994E-02 at 110iterations 4.7191826E-04 1.6250610E-02 at 120iterations finished qdiffx linear iterations at : 16:32:54 total time elapsed so far: 11.55000 # loops : 120 mean,max change (kT/e) : 4.7191826E-04 1.6250610E-02 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 16:32:54 11.728u 0.437s 0:12.43 97.7% 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 Sat Oct 8 2011 at 16:32:54 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: 355 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4549 !!! WARNING: GLM 203 has a net charge of -0.0940 !!! WARNING: FAD 991 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: 2.420269 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): 17.39100 80.96300 ymin,ymax (A): 118.6600 184.8510 zmin,zma (A): -1.200000 61.08000 x,y,z range (A): 63.57200 66.19099 62.28000 scale (grids/A): 2.420269 object centre (A): 49.17700 151.7555 29.94000 number of atom coordinates read : 4549 total number of charged atoms : 4359 net assigned charge : 3.906038 assigned positive charge : 696.3897 centred at (gu) : 98.61579 87.42252 77.03465 assigned negative charge : -692.4870 centred at (gu) : 98.47278 87.13789 77.11689 start vw surface at 0.1700000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 213139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41702 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 105214 mr = 150472 m= 36052 mr = 82775 m= 7013 mr = 27831 m= 554 mr = 4768 m= 8 mr = 230 m= 0 mr = 0 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.000000 number of dielectric boundary points 95904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 34815 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) : 1.613513 object centre at (A) : 49.17700 151.7555 29.94000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2273648E-02 0.1482661 midg,1,midg; midg,igrid,midg 0.1762773 0.5479966 1,midg,midg; igrid,midg,midg -0.1308983 -0.1403837 gauss-seidel spectral radius is 0.9992091 estimated iterations to convergence 281 setup time was (sec) 2.360000 now iterating at: 16:32:57 rms-change max change #iterations 11.01781 378.8757 at 10iterations 6.420542 154.8516 at 20iterations 3.703821 81.38277 at 30iterations 2.126167 44.58249 at 40iterations 1.218255 26.67148 at 50iterations 0.6958235 14.85561 at 60iterations 0.3964460 7.434128 at 70iterations 0.2245415 4.741806 at 80iterations 0.1272943 2.243327 at 90iterations 7.2232686E-02 1.359345 at 100iterations 4.0887758E-02 0.7040405 at 110iterations 2.3119610E-02 0.4093971 at 120iterations 1.3080020E-02 0.2478266 at 130iterations 7.3951636E-03 0.1413059 at 140iterations 4.1716946E-03 7.3213577E-02 at 150iterations 2.3566936E-03 4.0145874E-02 at 160iterations 1.3307839E-03 2.3483276E-02 at 170iterations 7.5197796E-04 1.4530182E-02 at 180iterations finished qdiffx linear iterations at : 16:33:14 total time elapsed so far: 19.43000 # loops : 180 mean,max change (kT/e) : 7.5197796E-04 1.4530182E-02 energy calculations done at 19.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.60000 DelPhi exited at 16:33:15 19.608u 0.481s 0:20.36 98.6% 0+0k 0+0io 0pf+0w