Sat Oct 8 16:27:14 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 Sat Oct 8 2011 at 16:27:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2304 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6495639 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): -6.990000 45.36100 ymin,ymax (A): -14.65500 29.50500 zmin,zma (A): -18.44100 36.36500 x,y,z range (A): 52.35100 44.16000 54.80600 scale (grids/A): 0.6495639 object centre (A): 19.18550 7.425000 8.961999 number of atom coordinates read : 2304 total number of charged atoms : 2242 net assigned charge : 5.000005 assigned positive charge : 344.2741 centred at (gu) : 91.86449 88.18484 90.06440 assigned negative charge : -339.2748 centred at (gu) : 91.93885 88.31345 90.09949 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6640 nv = 96 ne = 84 npr = 45874 no. pairs analyzed = 45874 no. exposed pairs = 2942 no. arc points = 20220 no. surface atoms = 1001 nbur = 1303 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 3637 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3500000 number of dielectric boundary points 3326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1992 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7968 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3743045E-08 4.8031357E-09 midg,1,midg; midg,igrid,midg 3.8228286E-08 -5.0988409E-09 1,midg,midg; igrid,midg,midg 1.2919816E-08 -1.0059514E-09 gauss-seidel spectral radius is 0.9876941 estimated iterations to convergence 74 setup time was (sec) 0.6400000 now iterating at: 16:27:15 rms-change max change #iterations 0.1412730 21.66114 at 10iterations 1.4567805E-02 2.168082 at 20iterations 1.5893957E-03 0.2893429 at 30iterations 2.1580876E-04 2.8089523E-02 at 40iterations 4.4474706E-05 7.0724487E-03 at 50iterations finished qdiffx linear iterations at : 16:27:19 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 4.4474706E-05 7.0724487E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.520000 DelPhi exited at 16:27:20 4.523u 0.461s 0:05.25 94.8% 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 Sat Oct 8 2011 at 16:27:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2304 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.948692 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): -6.990000 45.36100 ymin,ymax (A): -14.65500 29.50500 zmin,zma (A): -18.44100 36.36500 x,y,z range (A): 52.35100 44.16000 54.80600 scale (grids/A): 1.948692 object centre (A): 19.18550 7.425000 8.961999 number of atom coordinates read : 2304 total number of charged atoms : 2242 net assigned charge : 5.000005 assigned positive charge : 344.2741 centred at (gu) : 95.59289 84.55384 90.19292 assigned negative charge : -339.2748 centred at (gu) : 95.81661 84.94024 90.29835 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 71227 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20220 grid for indexing accessible points = 1.400000 m= 26093 mr = 49262 m= 4470 mr = 19202 m= 287 mr = 2827 m= 1 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 180 time to turn everything in is 0.7300000 number of dielectric boundary points 30698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 110 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 17687 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) : 0.6495639 object centre at (A) : 19.18550 7.425000 8.961999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1828079E-02 8.0863005E-03 midg,1,midg; midg,igrid,midg 2.6237324E-02 -5.9336466E-03 1,midg,midg; igrid,midg,midg 2.9250806E-02 -6.0679093E-02 gauss-seidel spectral radius is 0.9986644 estimated iterations to convergence 217 setup time was (sec) 1.060000 now iterating at: 16:27:21 rms-change max change #iterations 4.118327 177.6469 at 10iterations 1.943772 68.52840 at 20iterations 0.9191017 28.61328 at 30iterations 0.4366911 14.44932 at 40iterations 0.2054671 6.843632 at 50iterations 9.7657911E-02 3.286317 at 60iterations 4.5989677E-02 1.503391 at 70iterations 2.1828579E-02 0.7212677 at 80iterations 1.0310658E-02 0.3026733 at 90iterations 4.8853550E-03 0.1718235 at 100iterations 2.3173923E-03 7.5016022E-02 at 110iterations 1.1068445E-03 3.4914017E-02 at 120iterations finished qdiffx linear iterations at : 16:27:30 total time elapsed so far: 10.06000 # loops : 120 mean,max change (kT/e) : 1.1068445E-03 3.4914017E-02 energy calculations done at 10.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.27000 DelPhi exited at 16:27:31 10.274u 0.490s 0:11.03 97.5% 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 Sat Oct 8 2011 at 16:27:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2304 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.923038 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): -6.990000 45.36100 ymin,ymax (A): -14.65500 29.50500 zmin,zma (A): -18.44100 36.36500 x,y,z range (A): 52.35100 44.16000 54.80600 scale (grids/A): 2.923038 object centre (A): 19.18550 7.425000 8.961999 number of atom coordinates read : 2304 total number of charged atoms : 2242 net assigned charge : 5.000005 assigned positive charge : 344.2741 centred at (gu) : 98.38911 81.83072 90.28918 assigned negative charge : -339.2748 centred at (gu) : 98.72484 82.41042 90.44749 start vw surface at 0.1500000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 164909 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20220 grid for indexing accessible points = 1.400000 m= 83290 mr = 119949 m= 31675 mr = 67814 m= 8151 mr = 25494 m= 1207 mr = 6128 m= 68 mr = 781 m= 0 mr = 17 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 587 time to turn everything in is 1.940000 number of dielectric boundary points 69117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 17936 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) : 1.948692 object centre at (A) : 19.18550 7.425000 8.961999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4187959 8.7575920E-02 midg,1,midg; midg,igrid,midg 0.1918640 -8.2388163E-02 1,midg,midg; igrid,midg,midg 0.5865958 -0.8276879 gauss-seidel spectral radius is 0.9992664 estimated iterations to convergence 291 setup time was (sec) 2.300000 now iterating at: 16:27:33 rms-change max change #iterations 9.642895 382.0723 at 10iterations 5.665642 133.1312 at 20iterations 3.300680 66.64732 at 30iterations 1.928100 39.06511 at 40iterations 1.122382 22.67113 at 50iterations 0.6529167 12.76192 at 60iterations 0.3774368 7.223885 at 70iterations 0.2188052 4.323249 at 80iterations 0.1265279 2.315886 at 90iterations 7.3174179E-02 1.492778 at 100iterations 4.2224698E-02 0.8430443 at 110iterations 2.4367409E-02 0.4424181 at 120iterations 1.4055845E-02 0.2566200 at 130iterations 8.1426920E-03 0.1572876 at 140iterations 4.7029573E-03 8.8570118E-02 at 150iterations 2.7218892E-03 5.4362297E-02 at 160iterations 1.5851479E-03 2.8129578E-02 at 170iterations 9.2628237E-04 1.7026901E-02 at 180iterations finished qdiffx linear iterations at : 16:27:49 total time elapsed so far: 18.23000 # loops : 180 mean,max change (kT/e) : 9.2628237E-04 1.7026901E-02 energy calculations done at 18.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.45000 DelPhi exited at 16:27:50 18.452u 0.541s 0:19.26 98.5% 0+0k 0+0io 0pf+0w