Mon Oct 10 17:06:07 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 Mon Oct 10 2011 at 17:06:07 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: 377 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1835 !!! WARNING: HIR 119 has a net charge of 0.5140 !!! WARNING: HIT 148 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7040303 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): -26.47200 23.06300 ymin,ymax (A): -1.226000 38.29000 zmin,zma (A): 24.87100 75.43700 x,y,z range (A): 49.53500 39.51600 50.56600 scale (grids/A): 0.7040303 object centre (A): -1.704500 18.53200 50.15400 number of atom coordinates read : 1835 total number of charged atoms : 1706 net assigned charge : -4.471980 assigned positive charge : 267.2242 centred at (gu) : 88.08170 89.89840 91.46756 assigned negative charge : -271.6961 centred at (gu) : 88.15752 90.00097 91.53263 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6272 nv = 96 ne = 84 npr = 38242 no. pairs analyzed = 38242 no. exposed pairs = 2391 no. arc points = 17714 no. surface atoms = 804 nbur = 1031 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 334 mr = 3219 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2400000 number of dielectric boundary points 3341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1525 ## 118 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6887 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.3011623E-09 -8.1007549E-08 midg,1,midg; midg,igrid,midg 5.6000751E-09 -7.4424108E-08 1,midg,midg; igrid,midg,midg -6.1782885E-09 -4.5048040E-08 gauss-seidel spectral radius is 0.9894736 estimated iterations to convergence 79 setup time was (sec) 0.5300000 now iterating at: 17:06:08 rms-change max change #iterations 0.1889825 27.26620 at 10iterations 2.3356359E-02 3.274750 at 20iterations 2.7767881E-03 0.4242096 at 30iterations 3.3447100E-04 4.8953056E-02 at 40iterations 4.0280327E-05 6.5646172E-03 at 50iterations finished qdiffx linear iterations at : 17:06:11 total time elapsed so far: 4.410000 # loops : 50 mean,max change (kT/e) : 4.0280327E-05 6.5646172E-03 energy calculations done at 4.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.570000 DelPhi exited at 17:06:12 4.570u 0.383s 0:05.35 92.5% 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 17:06:12 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: 377 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1835 !!! WARNING: HIR 119 has a net charge of 0.5140 !!! WARNING: HIT 148 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.112091 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): -26.47200 23.06300 ymin,ymax (A): -1.226000 38.29000 zmin,zma (A): 24.87100 75.43700 x,y,z range (A): 49.53500 39.51600 50.56600 scale (grids/A): 2.112091 object centre (A): -1.704500 18.53200 50.15400 number of atom coordinates read : 1835 total number of charged atoms : 1706 net assigned charge : -4.471980 assigned positive charge : 267.2242 centred at (gu) : 84.24515 89.69533 94.40295 assigned negative charge : -271.6961 centred at (gu) : 84.47267 90.00311 94.59801 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 66571 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17714 grid for indexing accessible points = 1.400000 m= 23169 mr = 44144 m= 3940 mr = 16739 m= 325 mr = 2552 m= 13 mr = 161 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 178 time to turn everything in is 0.6200000 number of dielectric boundary points 30420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 13554 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) : 0.7040303 object centre at (A) : -1.704500 18.53200 50.15400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3519755E-02 -7.8349315E-02 midg,1,midg; midg,igrid,midg 1.6250154E-02 -1.6397534E-02 1,midg,midg; igrid,midg,midg 3.4920499E-02 1.9631825E-02 gauss-seidel spectral radius is 0.9988135 estimated iterations to convergence 230 setup time was (sec) 0.9300000 now iterating at: 17:06:13 rms-change max change #iterations 4.337674 275.8405 at 10iterations 2.120866 81.70203 at 20iterations 1.042165 34.26329 at 30iterations 0.5123850 17.91702 at 40iterations 0.2521401 7.854401 at 50iterations 0.1244949 4.138783 at 60iterations 6.1332855E-02 2.006432 at 70iterations 3.0038277E-02 1.047222 at 80iterations 1.4806162E-02 0.4547043 at 90iterations 7.2928853E-03 0.2337008 at 100iterations 3.5992798E-03 0.1170416 at 110iterations 1.7679200E-03 5.8486938E-02 at 120iterations finished qdiffx linear iterations at : 17:06:23 total time elapsed so far: 10.57000 # loops : 120 mean,max change (kT/e) : 1.7679200E-03 5.8486938E-02 energy calculations done at 10.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.72000 DelPhi exited at 17:06:24 10.726u 0.423s 0:11.49 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 Mon Oct 10 2011 at 17:06:24 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: 377 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1835 !!! WARNING: HIR 119 has a net charge of 0.5140 !!! WARNING: HIT 148 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.168137 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): -26.47200 23.06300 ymin,ymax (A): -1.226000 38.29000 zmin,zma (A): 24.87100 75.43700 x,y,z range (A): 49.53500 39.51600 50.56600 scale (grids/A): 3.168137 object centre (A): -1.704500 18.53200 50.15400 number of atom coordinates read : 1835 total number of charged atoms : 1706 net assigned charge : -4.471980 assigned positive charge : 267.2242 centred at (gu) : 81.36774 89.54318 96.60442 assigned negative charge : -271.6961 centred at (gu) : 81.70894 90.00465 96.89698 start vw surface at 0.1000000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 153790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17714 grid for indexing accessible points = 1.400000 m= 74492 mr = 107480 m= 27593 mr = 59896 m= 7259 mr = 22004 m= 1321 mr = 5551 m= 147 mr = 967 m= 8 mr = 102 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 628 time to turn everything in is 1.670000 number of dielectric boundary points 68604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 13648 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) : 2.112091 object centre at (A) : -1.704500 18.53200 50.15400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9439909 -0.7269872 midg,1,midg; midg,igrid,midg 0.1064865 -0.1072974 1,midg,midg; igrid,midg,midg 0.3289067 0.3199076 gauss-seidel spectral radius is 0.9993008 estimated iterations to convergence 298 setup time was (sec) 2.010000 now iterating at: 17:06:26 rms-change max change #iterations 9.587239 386.3425 at 10iterations 5.633619 135.5305 at 20iterations 3.313130 74.84627 at 30iterations 1.943145 43.05429 at 40iterations 1.135015 25.26678 at 50iterations 0.6656688 14.17727 at 60iterations 0.3887483 7.617134 at 70iterations 0.2271596 4.443207 at 80iterations 0.1324882 2.509583 at 90iterations 7.7145472E-02 1.479393 at 100iterations 4.5089517E-02 0.8277817 at 110iterations 2.6290750E-02 0.4382935 at 120iterations 1.5347848E-02 0.3098297 at 130iterations 8.9512039E-03 0.1619787 at 140iterations 5.2238638E-03 9.0955019E-02 at 150iterations 3.0474560E-03 5.3894043E-02 at 160iterations 1.7774024E-03 3.3344269E-02 at 170iterations 1.0419402E-03 1.9817352E-02 at 180iterations finished qdiffx linear iterations at : 17:06:43 total time elapsed so far: 18.57000 # loops : 180 mean,max change (kT/e) : 1.0419402E-03 1.9817352E-02 energy calculations done at 18.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.72000 DelPhi exited at 17:06:43 18.720u 0.457s 0:19.51 98.2% 0+0k 0+0io 0pf+0w