Tue Oct 11 01:09:35 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 Tue Oct 11 2011 at 01:09:35 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2746 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 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: 0.5745271 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): -6.403000 37.40400 ymin,ymax (A): -20.68600 41.27800 zmin,zma (A): 24.62800 77.36400 x,y,z range (A): 43.80700 61.96400 52.73600 scale (grids/A): 0.5745271 object centre (A): 15.50050 10.29600 50.99600 number of atom coordinates read : 2746 total number of charged atoms : 2594 net assigned charge : 5.312016 assigned positive charge : 414.4296 centred at (gu) : 90.15846 89.03383 89.43563 assigned negative charge : -409.1182 centred at (gu) : 90.36652 89.22344 89.41563 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5888 nv = 96 ne = 84 npr = 55820 no. pairs analyzed = 55820 no. exposed pairs = 3220 no. arc points = 22888 no. surface atoms = 1093 nbur = 1653 mkacc time = 0.1400000 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 = 1.484000 m= 233 mr = 3261 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.3100000 number of dielectric boundary points 2839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2334 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7568 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8028116E-10 1.1187410E-09 midg,1,midg; midg,igrid,midg 5.1191642E-09 -1.8428451E-09 1,midg,midg; igrid,midg,midg 4.1992161E-09 -2.7651972E-09 gauss-seidel spectral radius is 0.9843422 estimated iterations to convergence 66 setup time was (sec) 0.5700000 now iterating at: 01:09:36 rms-change max change #iterations 9.3308136E-02 15.21656 at 10iterations 7.8612166E-03 1.398132 at 20iterations 9.5209485E-04 0.2332497 at 30iterations 2.0548877E-04 5.3993225E-02 at 40iterations 4.7823403E-05 1.3183594E-02 at 50iterations finished qdiffx linear iterations at : 01:09:40 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 4.7823403E-05 1.3183594E-02 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 01:09:40 4.446u 0.392s 0:05.15 93.7% 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 Tue Oct 11 2011 at 01:09:40 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2746 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 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: 1.723581 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): -6.403000 37.40400 ymin,ymax (A): -20.68600 41.27800 zmin,zma (A): 24.62800 77.36400 x,y,z range (A): 43.80700 61.96400 52.73600 scale (grids/A): 1.723581 object centre (A): 15.50050 10.29600 50.99600 number of atom coordinates read : 2746 total number of charged atoms : 2594 net assigned charge : 5.312016 assigned positive charge : 414.4296 centred at (gu) : 90.47487 87.10072 88.30624 assigned negative charge : -409.1182 centred at (gu) : 91.09933 87.66982 88.24681 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 64978 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22888 grid for indexing accessible points = 1.400000 m= 20583 mr = 45216 m= 2398 mr = 14908 m= 69 mr = 1381 m= 0 mr = 11 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 4422 time to turn everything in is 0.5100000 number of dielectric boundary points 26512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 20097 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) : 0.5745271 object centre at (A) : 15.50050 10.29600 50.99600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4362721E-03 9.4669210E-03 midg,1,midg; midg,igrid,midg -1.4995903E-02 -9.7971931E-03 1,midg,midg; igrid,midg,midg 2.0584358E-02 -1.0517264E-03 gauss-seidel spectral radius is 0.9983473 estimated iterations to convergence 195 setup time was (sec) 0.8200000 now iterating at: 01:09:41 rms-change max change #iterations 3.582401 153.0044 at 10iterations 1.551918 65.39742 at 20iterations 0.6758004 24.30816 at 30iterations 0.2925078 11.76403 at 40iterations 0.1272391 5.131550 at 50iterations 5.5293053E-02 2.165833 at 60iterations 2.4195813E-02 0.8616810 at 70iterations 1.0649887E-02 0.4125366 at 80iterations 4.7315815E-03 0.1601410 at 90iterations 2.1564339E-03 7.7968597E-02 at 100iterations 1.0327577E-03 4.5989990E-02 at 110iterations 5.3168926E-04 2.5260925E-02 at 120iterations finished qdiffx linear iterations at : 01:09:51 total time elapsed so far: 10.49000 # loops : 120 mean,max change (kT/e) : 5.3168926E-04 2.5260925E-02 energy calculations done at 10.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.66000 DelPhi exited at 01:09:52 10.661u 0.449s 0:11.41 97.2% 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 01:09:52 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2746 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 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: 2.585372 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): -6.403000 37.40400 ymin,ymax (A): -20.68600 41.27800 zmin,zma (A): 24.62800 77.36400 x,y,z range (A): 43.80700 61.96400 52.73600 scale (grids/A): 2.585372 object centre (A): 15.50050 10.29600 50.99600 number of atom coordinates read : 2746 total number of charged atoms : 2594 net assigned charge : 5.312016 assigned positive charge : 414.4296 centred at (gu) : 90.71207 85.65105 87.45921 assigned negative charge : -409.1182 centred at (gu) : 91.64883 86.50456 87.37019 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 150816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22888 grid for indexing accessible points = 1.400000 m= 70670 mr = 110009 m= 21367 mr = 57553 m= 3968 mr = 16767 m= 343 mr = 2902 m= 6 mr = 182 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 14822 time to turn everything in is 1.310000 number of dielectric boundary points 59757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 20743 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) : 1.723581 object centre at (A) : 15.50050 10.29600 50.99600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9618941E-02 8.8176213E-02 midg,1,midg; midg,igrid,midg -0.5804506 -0.1354702 1,midg,midg; igrid,midg,midg 0.2407925 2.0345967E-02 gauss-seidel spectral radius is 0.9991738 estimated iterations to convergence 275 setup time was (sec) 1.640000 now iterating at: 01:09:54 rms-change max change #iterations 8.859964 258.6573 at 10iterations 4.948970 121.0160 at 20iterations 2.774291 61.58843 at 30iterations 1.550824 35.82111 at 40iterations 0.8624610 17.61988 at 50iterations 0.4825660 10.23869 at 60iterations 0.2672930 5.586803 at 70iterations 0.1491477 3.135915 at 80iterations 8.3090946E-02 1.845377 at 90iterations 4.6190999E-02 0.9520550 at 100iterations 2.5809925E-02 0.4982986 at 110iterations 1.4398997E-02 0.3012085 at 120iterations 8.0758594E-03 0.1677818 at 130iterations 4.5644944E-03 9.5687866E-02 at 140iterations 2.6081526E-03 7.0331573E-02 at 150iterations 1.5317447E-03 4.1213989E-02 at 160iterations 9.3173311E-04 2.4814606E-02 at 170iterations 5.9293944E-04 1.6078949E-02 at 180iterations finished qdiffx linear iterations at : 01:10:09 total time elapsed so far: 17.08000 # loops : 180 mean,max change (kT/e) : 5.9293944E-04 1.6078949E-02 energy calculations done at 17.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.23000 DelPhi exited at 01:10:10 17.239u 0.449s 0:18.31 96.5% 0+0k 0+0io 0pf+0w