Tue Oct 11 06:52:37 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 06:52:37 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 0.5453265 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): -20.13600 45.14600 ymin,ymax (A): 19.46500 77.06200 zmin,zma (A): -70.01700 -20.11100 x,y,z range (A): 65.28200 57.59700 49.90600 scale (grids/A): 0.5453265 object centre (A): 12.50500 48.26350 -45.06400 number of atom coordinates read : 3002 total number of charged atoms : 2855 net assigned charge : -5.040987 assigned positive charge : 439.7835 centred at (gu) : 89.59586 89.52579 89.54313 assigned negative charge : -444.8251 centred at (gu) : 89.60616 89.72414 89.55626 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5825 nv = 96 ne = 84 npr = 62103 no. pairs analyzed = 62103 no. exposed pairs = 3733 no. arc points = 26809 no. surface atoms = 1258 nbur = 1744 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 = 1.568000 m= 216 mr = 2993 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.4300000 number of dielectric boundary points 3044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2705 ## 327 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 7594 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5301286E-10 -3.5584766E-10 midg,1,midg; midg,igrid,midg 1.0658050E-09 -1.4503804E-09 1,midg,midg; igrid,midg,midg -2.7014657E-10 -3.4376310E-10 gauss-seidel spectral radius is 0.9826691 estimated iterations to convergence 63 setup time was (sec) 0.7200000 now iterating at: 06:52:38 rms-change max change #iterations 7.3337860E-02 13.65106 at 10iterations 4.9211360E-03 0.8248653 at 20iterations 3.2633473E-04 4.7985077E-02 at 30iterations 2.1295858E-05 3.7155151E-03 at 40iterations 1.4531091E-06 2.4795532E-04 at 50iterations finished qdiffx linear iterations at : 06:52:42 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 1.4531091E-06 2.4795532E-04 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 06:52:43 4.538u 0.398s 0:05.25 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 06:52:43 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 # of charge parameter records: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 1.635979 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): -20.13600 45.14600 ymin,ymax (A): 19.46500 77.06200 zmin,zma (A): -70.01700 -20.11100 x,y,z range (A): 65.28200 57.59700 49.90600 scale (grids/A): 1.635979 object centre (A): 12.50500 48.26350 -45.06400 number of atom coordinates read : 3002 total number of charged atoms : 2855 net assigned charge : -5.040987 assigned positive charge : 439.7835 centred at (gu) : 88.78731 88.57655 88.62884 assigned negative charge : -444.8251 centred at (gu) : 88.81788 89.17217 88.66834 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 63980 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26809 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20279 mr = 42996 m= 2136 mr = 14194 m= 49 mr = 1109 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 697 time to turn everything in is 0.6700000 number of dielectric boundary points 28145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 276 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 21876 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) : 0.5453265 object centre at (A) : 12.50500 48.26350 -45.06400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6774583E-03 6.9186622E-03 midg,1,midg; midg,igrid,midg -1.9353090E-05 -5.4395841E-03 1,midg,midg; igrid,midg,midg -1.1261394E-03 -3.2725215E-02 gauss-seidel spectral radius is 0.9982010 estimated iterations to convergence 187 setup time was (sec) 0.9900000 now iterating at: 06:52:44 rms-change max change #iterations 3.320569 158.1142 at 10iterations 1.384798 59.37309 at 20iterations 0.5832841 26.87540 at 30iterations 0.2443193 9.860199 at 40iterations 0.1018785 4.439972 at 50iterations 4.2550668E-02 1.701698 at 60iterations 1.7838106E-02 0.6007786 at 70iterations 7.4550356E-03 0.2848263 at 80iterations 3.1375901E-03 0.1307220 at 90iterations 1.3120446E-03 4.5574188E-02 at 100iterations 5.4929237E-04 2.0113230E-02 at 110iterations 2.2996544E-04 8.4936619E-03 at 120iterations finished qdiffx linear iterations at : 06:52:53 total time elapsed so far: 9.990000 # loops : 120 mean,max change (kT/e) : 2.2996544E-04 8.4936619E-03 energy calculations done at 9.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.19000 DelPhi exited at 06:52:54 10.196u 0.447s 0:10.97 96.9% 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 Tue Oct 11 2011 at 06:52:54 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 2.453969 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): -20.13600 45.14600 ymin,ymax (A): 19.46500 77.06200 zmin,zma (A): -70.01700 -20.11100 x,y,z range (A): 65.28200 57.59700 49.90600 scale (grids/A): 2.453969 object centre (A): 12.50500 48.26350 -45.06400 number of atom coordinates read : 3002 total number of charged atoms : 2855 net assigned charge : -5.040987 assigned positive charge : 439.7835 centred at (gu) : 88.18091 87.86459 87.94312 assigned negative charge : -444.8251 centred at (gu) : 88.22675 88.75814 88.00239 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 148100 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26809 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 69156 mr = 104881 m= 20832 mr = 54966 m= 3334 mr = 16007 m= 231 mr = 2235 m= 2 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 2310 time to turn everything in is 1.640000 number of dielectric boundary points 63465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 22811 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) : 1.635979 object centre at (A) : 12.50500 48.26350 -45.06400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6009752E-02 0.1748505 midg,1,midg; midg,igrid,midg 9.4072567E-04 -1.7693514E-02 1,midg,midg; igrid,midg,midg -6.8384707E-02 -0.6230745 gauss-seidel spectral radius is 0.9991470 estimated iterations to convergence 270 setup time was (sec) 2.010000 now iterating at: 06:52:56 rms-change max change #iterations 8.586452 348.1641 at 10iterations 4.838549 144.6346 at 20iterations 2.701169 66.59297 at 30iterations 1.502605 33.37517 at 40iterations 0.8355460 18.86070 at 50iterations 0.4615201 11.76220 at 60iterations 0.2558770 5.413029 at 70iterations 0.1414177 2.871971 at 80iterations 7.8003839E-02 1.593296 at 90iterations 4.2934008E-02 0.8726349 at 100iterations 2.3730237E-02 0.5481796 at 110iterations 1.3031473E-02 0.2670269 at 120iterations 7.1986723E-03 0.1651306 at 130iterations 3.9650821E-03 8.0291748E-02 at 140iterations 2.1848984E-03 4.7277927E-02 at 150iterations 1.2013441E-03 2.5746346E-02 at 160iterations 6.6064112E-04 1.2457848E-02 at 170iterations 3.6428336E-04 7.5302124E-03 at 180iterations finished qdiffx linear iterations at : 06:53:11 total time elapsed so far: 16.72000 # loops : 180 mean,max change (kT/e) : 3.6428336E-04 7.5302124E-03 energy calculations done at 16.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.94000 DelPhi exited at 06:53:12 16.943u 0.443s 0:17.94 96.8% 0+0k 0+0io 0pf+0w