Tue Oct 11 07:13:34 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 07:13:34 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3205 !!! WARNING: HIR 51 has a net charge of 0.5140 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 0.5933135 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): 0.3160000 48.70600 ymin,ymax (A): -9.035000 49.16200 zmin,zma (A): 0.8770000 60.87900 x,y,z range (A): 48.39000 58.19700 60.00200 scale (grids/A): 0.5933135 object centre (A): 24.51100 20.06350 30.87800 number of atom coordinates read : 3205 total number of charged atoms : 3060 net assigned charge : -2.085990 assigned positive charge : 483.0609 centred at (gu) : 89.61959 89.62242 90.85606 assigned negative charge : -485.1480 centred at (gu) : 89.54218 89.55453 90.80215 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7505 nv = 96 ne = 84 npr = 66145 no. pairs analyzed = 66145 no. exposed pairs = 3725 no. arc points = 25397 no. surface atoms = 1267 nbur = 1938 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 329 mr = 4379 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.3500000 number of dielectric boundary points 3413 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2602 ## 252 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9438 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2323086E-09 1.5623541E-09 midg,1,midg; midg,igrid,midg -3.5371872E-09 1.6273043E-09 1,midg,midg; igrid,midg,midg -3.9306034E-09 1.9427278E-09 gauss-seidel spectral radius is 0.9853458 estimated iterations to convergence 68 setup time was (sec) 0.6000000 now iterating at: 07:13:35 rms-change max change #iterations 0.1180151 19.67924 at 10iterations 1.0216049E-02 1.429278 at 20iterations 1.0679305E-03 0.1756763 at 30iterations 1.8091379E-04 2.9016495E-02 at 40iterations 4.1247466E-05 7.0533752E-03 at 50iterations finished qdiffx linear iterations at : 07:13:38 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 4.1247466E-05 7.0533752E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 07:13:39 3.643u 0.215s 0:04.38 87.8% 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 Tue Oct 11 2011 at 07:13:39 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3205 !!! WARNING: HIR 51 has a net charge of 0.5140 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 1.779941 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): 0.3160000 48.70600 ymin,ymax (A): -9.035000 49.16200 zmin,zma (A): 0.8770000 60.87900 x,y,z range (A): 48.39000 58.19700 60.00200 scale (grids/A): 1.779941 object centre (A): 24.51100 20.06350 30.87800 number of atom coordinates read : 3205 total number of charged atoms : 3060 net assigned charge : -2.085990 assigned positive charge : 483.0609 centred at (gu) : 88.85806 88.86674 92.56757 assigned negative charge : -485.1480 centred at (gu) : 88.62637 88.66315 92.40582 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 82498 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25397 grid for indexing accessible points = 1.400000 m= 29987 mr = 59586 m= 4077 mr = 22913 m= 159 mr = 2576 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 2669 time to turn everything in is 0.6200000 number of dielectric boundary points 31610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 231 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 23888 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) : 0.5933135 object centre at (A) : 24.51100 20.06350 30.87800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2216096E-02 1.8076723E-03 midg,1,midg; midg,igrid,midg -1.4888571E-02 1.0330381E-03 1,midg,midg; igrid,midg,midg -1.2290836E-02 5.3901915E-03 gauss-seidel spectral radius is 0.9984984 estimated iterations to convergence 205 setup time was (sec) 0.9500000 now iterating at: 07:13:40 rms-change max change #iterations 4.205666 172.6245 at 10iterations 1.898519 64.85795 at 20iterations 0.8603751 27.69349 at 30iterations 0.3894000 12.56142 at 40iterations 0.1759985 5.425819 at 50iterations 7.9731472E-02 2.546894 at 60iterations 3.6085166E-02 1.184715 at 70iterations 1.6381687E-02 0.5685120 at 80iterations 7.4099456E-03 0.2450600 at 90iterations 3.3762811E-03 0.1007214 at 100iterations 1.5394327E-03 4.6586990E-02 at 110iterations 7.0860196E-04 2.4164200E-02 at 120iterations finished qdiffx linear iterations at : 07:13:47 total time elapsed so far: 8.020000 # loops : 120 mean,max change (kT/e) : 7.0860196E-04 2.4164200E-02 energy calculations done at 8.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.210000 DelPhi exited at 07:13:48 8.215u 0.216s 0:08.74 96.3% 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 Tue Oct 11 2011 at 07:13:48 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3205 !!! WARNING: HIR 51 has a net charge of 0.5140 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 2.669911 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): 0.3160000 48.70600 ymin,ymax (A): -9.035000 49.16200 zmin,zma (A): 0.8770000 60.87900 x,y,z range (A): 48.39000 58.19700 60.00200 scale (grids/A): 2.669911 object centre (A): 24.51100 20.06350 30.87800 number of atom coordinates read : 3205 total number of charged atoms : 3060 net assigned charge : -2.085990 assigned positive charge : 483.0609 centred at (gu) : 88.28687 88.29974 93.85113 assigned negative charge : -485.1480 centred at (gu) : 87.93952 87.99458 93.60865 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 191134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25397 grid for indexing accessible points = 1.400000 m= 99273 mr = 144050 m= 33994 mr = 83140 m= 7019 mr = 27841 m= 807 mr = 5392 m= 33 mr = 577 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 9009 time to turn everything in is 1.530000 number of dielectric boundary points 71250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 24477 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) : 1.779941 object centre at (A) : 24.51100 20.06350 30.87800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3489061 -8.2507752E-02 midg,1,midg; midg,igrid,midg -0.3051362 3.5667054E-02 1,midg,midg; igrid,midg,midg -0.1397281 8.2718723E-02 gauss-seidel spectral radius is 0.9992270 estimated iterations to convergence 284 setup time was (sec) 1.870000 now iterating at: 07:13:50 rms-change max change #iterations 10.13612 287.0678 at 10iterations 5.843729 117.0326 at 20iterations 3.348965 76.46948 at 30iterations 1.909197 38.12792 at 40iterations 1.089043 19.71517 at 50iterations 0.6217006 10.93508 at 60iterations 0.3542401 5.892913 at 70iterations 0.2015583 3.588047 at 80iterations 0.1144658 2.025234 at 90iterations 6.4979061E-02 1.169239 at 100iterations 3.7007760E-02 0.6127167 at 110iterations 2.0977227E-02 0.3418134 at 120iterations 1.1932003E-02 0.2049545 at 130iterations 6.8045487E-03 0.1261688 at 140iterations 3.8760088E-03 6.5774918E-02 at 150iterations 2.2183659E-03 4.2201996E-02 at 160iterations 1.2716793E-03 2.3559570E-02 at 170iterations 7.3952734E-04 1.4034510E-02 at 180iterations finished qdiffx linear iterations at : 07:14:01 total time elapsed so far: 13.14000 # loops : 180 mean,max change (kT/e) : 7.3952734E-04 1.4034510E-02 energy calculations done at 13.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 07:14:02 13.331u 0.254s 0:13.89 97.7% 0+0k 0+0io 0pf+0w