Mon Oct 10 10:39:56 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 10:39:56 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5043 !!! WARNING: NAP 1619 has a net charge of -2.0000 !!! WARNING: NAP 1620 has a net charge of -2.0000 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: 0.5414696 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): -45.42600 10.69200 ymin,ymax (A): -26.55600 39.19100 zmin,zma (A): -4.230000 58.07200 x,y,z range (A): 56.11800 65.74700 62.30200 scale (grids/A): 0.5414696 object centre (A): -17.36700 6.317501 26.92100 number of atom coordinates read : 5043 total number of charged atoms : 4943 net assigned charge : 7.500004 assigned positive charge : 805.8070 centred at (gu) : 90.45623 90.31793 89.80065 assigned negative charge : -798.3143 centred at (gu) : 90.46432 90.35850 89.84821 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 9718 nv = 96 ne = 84 npr = 98365 no. pairs analyzed = 98365 no. exposed pairs = 6079 no. arc points = 40754 no. surface atoms = 2038 nbur = 3005 mkacc time = 0.2600000 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= 399 mr = 5546 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.5200000 number of dielectric boundary points 4551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4088 ## 504 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 12719 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1194557E-10 -8.5018471E-11 midg,1,midg; midg,igrid,midg 7.3773748E-10 -2.2280316E-11 1,midg,midg; igrid,midg,midg 4.2331141E-10 3.4591685E-10 gauss-seidel spectral radius is 0.9825691 estimated iterations to convergence 62 setup time was (sec) 0.8400000 now iterating at: 10:39:57 rms-change max change #iterations 9.7453743E-02 12.96968 at 10iterations 6.9778105E-03 0.9034233 at 20iterations 1.2682262E-03 0.1823368 at 30iterations 6.3450466E-04 9.1918945E-02 at 40iterations 3.4860984E-04 4.9351692E-02 at 50iterations finished qdiffx linear iterations at : 10:40:01 total time elapsed so far: 4.630000 # loops : 50 mean,max change (kT/e) : 3.4860984E-04 4.9351692E-02 energy calculations done at 4.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.800000 DelPhi exited at 10:40:02 4.803u 0.424s 0:05.82 89.6% 0+0k 0+0io 6pf+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 10:40:02 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5043 !!! WARNING: NAP 1619 has a net charge of -2.0000 !!! WARNING: NAP 1620 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.624409 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): -45.42600 10.69200 ymin,ymax (A): -26.55600 39.19100 zmin,zma (A): -4.230000 58.07200 x,y,z range (A): 56.11800 65.74700 62.30200 scale (grids/A): 1.624409 object centre (A): -17.36700 6.317501 26.92100 number of atom coordinates read : 5043 total number of charged atoms : 4943 net assigned charge : 7.500004 assigned positive charge : 805.8070 centred at (gu) : 91.36680 90.95210 89.39979 assigned negative charge : -798.3143 centred at (gu) : 91.39277 91.07549 89.54478 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 110171 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40754 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 36142 mr = 80144 m= 3763 mr = 25717 m= 94 mr = 1895 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 2448 time to turn everything in is 0.8700000 number of dielectric boundary points 42403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 452 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 37809 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) : 0.5414696 object centre at (A) : -17.36700 6.317501 26.92100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5956828E-02 7.0708594E-03 midg,1,midg; midg,igrid,midg -2.5245283E-02 -9.1911368E-03 1,midg,midg; igrid,midg,midg 2.4084222E-02 8.8739283E-03 gauss-seidel spectral radius is 0.9983714 estimated iterations to convergence 197 setup time was (sec) 1.190000 now iterating at: 10:40:03 rms-change max change #iterations 4.688874 271.2604 at 10iterations 2.051126 71.10579 at 20iterations 0.8943293 30.29607 at 30iterations 0.3920370 14.59134 at 40iterations 0.1714645 5.512070 at 50iterations 7.5417340E-02 2.071249 at 60iterations 3.3099297E-02 0.9718018 at 70iterations 1.4634063E-02 0.4293442 at 80iterations 6.5277014E-03 0.1954994 at 90iterations 3.0414306E-03 9.9720001E-02 at 100iterations 1.5516570E-03 5.6541443E-02 at 110iterations 9.3389052E-04 3.2544136E-02 at 120iterations finished qdiffx linear iterations at : 10:40:14 total time elapsed so far: 11.30000 # loops : 120 mean,max change (kT/e) : 9.3389052E-04 3.2544136E-02 energy calculations done at 11.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.46000 DelPhi exited at 10:40:14 11.469u 0.477s 0:12.28 97.1% 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 10:40:14 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5043 !!! WARNING: NAP 1619 has a net charge of -2.0000 !!! WARNING: NAP 1620 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.436613 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): -45.42600 10.69200 ymin,ymax (A): -26.55600 39.19100 zmin,zma (A): -4.230000 58.07200 x,y,z range (A): 56.11800 65.74700 62.30200 scale (grids/A): 2.436613 object centre (A): -17.36700 6.317501 26.92100 number of atom coordinates read : 5043 total number of charged atoms : 4943 net assigned charge : 7.500004 assigned positive charge : 805.8070 centred at (gu) : 92.04971 91.42781 89.09922 assigned negative charge : -798.3143 centred at (gu) : 92.08904 91.61311 89.31709 start vw surface at 0.1700000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 256857 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40754 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 125632 mr = 195379 m= 35987 mr = 101937 m= 5792 mr = 27538 m= 397 mr = 3788 m= 6 mr = 207 m= 0 mr = 0 time to grow re-entrant surface = 1.410000 no. cavity mid-points inaccessible to solvent = 8682 time to turn everything in is 2.220000 number of dielectric boundary points 95822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 2.380000 number of grid points assigned charge 39490 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) : 1.624409 object centre at (A) : -17.36700 6.317501 26.92100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1770485 0.1011994 midg,1,midg; midg,igrid,midg -0.4761269 -0.1383513 1,midg,midg; igrid,midg,midg 0.3843798 0.1556677 gauss-seidel spectral radius is 0.9992375 estimated iterations to convergence 286 setup time was (sec) 2.580000 now iterating at: 10:40:17 rms-change max change #iterations 12.09770 359.9056 at 10iterations 7.117580 155.7321 at 20iterations 4.160089 82.84375 at 30iterations 2.419010 50.63330 at 40iterations 1.401547 26.60831 at 50iterations 0.8090826 16.40992 at 60iterations 0.4666722 8.932886 at 70iterations 0.2686100 5.315266 at 80iterations 0.1542906 2.899343 at 90iterations 8.8627048E-02 1.970393 at 100iterations 5.0775465E-02 1.036849 at 110iterations 2.9133396E-02 0.5746040 at 120iterations 1.6713474E-02 0.3136215 at 130iterations 9.5755132E-03 0.1615534 at 140iterations 5.5023506E-03 9.1707230E-02 at 150iterations 3.1909051E-03 4.9298763E-02 at 160iterations 1.8639128E-03 3.1578064E-02 at 170iterations 1.1184833E-03 1.9918442E-02 at 180iterations finished qdiffx linear iterations at : 10:40:35 total time elapsed so far: 20.01000 # loops : 180 mean,max change (kT/e) : 1.1184833E-03 1.9918442E-02 energy calculations done at 20.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.18000 DelPhi exited at 10:40:35 20.181u 0.499s 0:21.10 97.9% 0+0k 0+0io 0pf+0w