Mon Oct 10 17:01:20 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 Mon Oct 10 2011 at 17:01:21 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4829 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5124072 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): -18.84500 37.78600 ymin,ymax (A): -30.61900 35.68600 zmin,zma (A): -4.138000 65.33800 x,y,z range (A): 56.63100 66.30500 69.47600 scale (grids/A): 0.5124072 object centre (A): 9.470502 2.533501 30.60000 number of atom coordinates read : 4829 total number of charged atoms : 4582 net assigned charge : 6.800047 assigned positive charge : 725.7622 centred at (gu) : 90.08612 90.10393 88.45141 assigned negative charge : -718.9670 centred at (gu) : 89.97639 90.17664 88.44437 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8105 nv = 96 ne = 84 npr = 97049 no. pairs analyzed = 97049 no. exposed pairs = 6205 no. arc points = 42760 no. surface atoms = 2082 nbur = 2747 mkacc time = 0.2100000 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 = 1.652000 m= 282 mr = 4141 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4170 ## 593 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10719 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2606104E-10 8.3994749E-11 midg,1,midg; midg,igrid,midg 2.9915009E-10 -1.0476998E-10 1,midg,midg; igrid,midg,midg -2.0365454E-10 4.1847431E-10 gauss-seidel spectral radius is 0.9805286 estimated iterations to convergence 59 setup time was (sec) 0.6400000 now iterating at: 17:01:21 rms-change max change #iterations 7.0234187E-02 11.38217 at 10iterations 4.9936092E-03 0.8476791 at 20iterations 9.5531030E-04 0.1389656 at 30iterations 3.5062383E-04 4.2491913E-02 at 40iterations 1.4138395E-04 1.8044949E-02 at 50iterations finished qdiffx linear iterations at : 17:01:24 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 1.4138395E-04 1.8044949E-02 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 17:01:24 3.241u 0.168s 0:04.33 78.5% 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 17:01:25 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4829 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.537222 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): -18.84500 37.78600 ymin,ymax (A): -30.61900 35.68600 zmin,zma (A): -4.138000 65.33800 x,y,z range (A): 56.63100 66.30500 69.47600 scale (grids/A): 1.537222 object centre (A): 9.470502 2.533501 30.60000 number of atom coordinates read : 4829 total number of charged atoms : 4582 net assigned charge : 6.800047 assigned positive charge : 725.7622 centred at (gu) : 90.25695 90.31017 85.35287 assigned negative charge : -718.9670 centred at (gu) : 89.92886 90.52965 85.33304 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 91667 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42760 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26674 mr = 62863 m= 2315 mr = 17548 m= 52 mr = 921 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 39376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 587 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 34556 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) : 0.5124072 object centre at (A) : 9.470502 2.533501 30.60000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0662750E-03 1.7749541E-02 midg,1,midg; midg,igrid,midg 1.0979636E-02 -1.2065414E-02 1,midg,midg; igrid,midg,midg -1.2105610E-03 1.3097753E-02 gauss-seidel spectral radius is 0.9981379 estimated iterations to convergence 184 setup time was (sec) 0.9100000 now iterating at: 17:01:26 rms-change max change #iterations 3.865392 143.5726 at 10iterations 1.588491 54.82436 at 20iterations 0.6596103 21.10608 at 30iterations 0.2721064 8.864617 at 40iterations 0.1127261 3.639763 at 50iterations 4.6492659E-02 1.532204 at 60iterations 1.9344248E-02 0.6328192 at 70iterations 8.1262970E-03 0.3009644 at 80iterations 3.4981354E-03 0.1110973 at 90iterations 1.5826173E-03 5.4239985E-02 at 100iterations 8.0514635E-04 2.6373863E-02 at 110iterations 4.6801937E-04 1.3996124E-02 at 120iterations finished qdiffx linear iterations at : 17:01:32 total time elapsed so far: 6.950000 # loops : 120 mean,max change (kT/e) : 4.6801937E-04 1.3996124E-02 energy calculations done at 6.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.120000 DelPhi exited at 17:01:33 7.128u 0.200s 0:07.80 93.8% 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 17:01:33 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4829 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.305832 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): -18.84500 37.78600 ymin,ymax (A): -30.61900 35.68600 zmin,zma (A): -4.138000 65.33800 x,y,z range (A): 56.63100 66.30500 69.47600 scale (grids/A): 2.305832 object centre (A): 9.470502 2.533501 30.60000 number of atom coordinates read : 4829 total number of charged atoms : 4582 net assigned charge : 6.800047 assigned positive charge : 725.7622 centred at (gu) : 90.38509 90.46497 83.02903 assigned negative charge : -718.9670 centred at (gu) : 89.89326 90.79430 82.99960 start vw surface at 0.2100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 213374 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42760 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 95988 mr = 154383 m= 24124 mr = 74639 m= 3352 mr = 17064 m= 216 mr = 1940 m= 7 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.500000 number of dielectric boundary points 88955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 36557 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) : 1.537222 object centre at (A) : 9.470502 2.533501 30.60000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1313151 0.4650243 midg,1,midg; midg,igrid,midg 0.1228124 -0.3024803 1,midg,midg; igrid,midg,midg -1.0288078E-02 0.1924543 gauss-seidel spectral radius is 0.9991750 estimated iterations to convergence 275 setup time was (sec) 1.780000 now iterating at: 17:01:35 rms-change max change #iterations 10.43504 296.0748 at 10iterations 6.024103 137.7480 at 20iterations 3.445826 69.80166 at 30iterations 1.959569 42.47732 at 40iterations 1.110810 23.60246 at 50iterations 0.6266478 12.55871 at 60iterations 0.3529957 7.269852 at 70iterations 0.1984137 4.307642 at 80iterations 0.1114836 2.205544 at 90iterations 6.2452853E-02 1.357117 at 100iterations 3.5033420E-02 0.6637735 at 110iterations 1.9572187E-02 0.3791428 at 120iterations 1.0950152E-02 0.1970282 at 130iterations 6.1235288E-03 0.1167033 at 140iterations 3.4245942E-03 7.6372683E-02 at 150iterations 1.9177488E-03 3.7912369E-02 at 160iterations 1.0827400E-03 2.1604538E-02 at 170iterations 6.1201130E-04 1.2578011E-02 at 180iterations finished qdiffx linear iterations at : 17:01:44 total time elapsed so far: 11.34000 # loops : 180 mean,max change (kT/e) : 6.1201130E-04 1.2578011E-02 energy calculations done at 11.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.51000 DelPhi exited at 17:01:45 11.513u 0.166s 0:12.16 95.9% 0+0k 0+0io 0pf+0w