Sat Oct 15 11:28:02 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 Sat Oct 15 2011 at 11:28:02 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5009 !!! WARNING: GLM 203 has a net charge of -0.0940 !!! WARNING: FAD 4965 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: 0.2614379 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): -24.31100 75.55400 ymin,ymax (A): -25.78700 95.90200 zmin,zma (A): -23.58200 112.5880 x,y,z range (A): 99.86501 121.6890 136.1700 scale (grids/A): 0.2614379 object centre (A): 25.62150 35.05750 44.50300 number of atom coordinates read : 5009 total number of charged atoms : 4391 net assigned charge : 1.406037 assigned positive charge : 702.2128 centred at (gu) : 84.76148 84.19302 81.08295 assigned negative charge : -700.8102 centred at (gu) : 84.80222 84.23557 81.10836 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 1747 nv = 96 ne = 84 npr = 94919 no. pairs analyzed = 94919 no. exposed pairs = 6798 no. arc points = 51322 no. surface atoms = 2305 nbur = 2704 mkacc time = 0.2200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 3.261440 m= 28 mr = 572 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 1203 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1573 ## 611 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 2249 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7166354E-18 -6.8872651E-22 midg,1,midg; midg,igrid,midg 1.2303462E-18 -4.6217566E-21 1,midg,midg; igrid,midg,midg 8.6837969E-19 -5.7911254E-21 gauss-seidel spectral radius is 0.9278851 estimated iterations to convergence 32 setup time was (sec) 0.7400000 now iterating at: 11:28:03 rms-change max change #iterations 1.6094018E-03 0.6732712 at 10iterations 1.7357002E-04 7.4208736E-02 at 20iterations 2.5904770E-05 1.1506081E-02 at 30iterations 3.9047882E-06 1.7580986E-03 at 40iterations 5.9035784E-07 2.6750565E-04 at 50iterations finished qdiffx linear iterations at : 11:28:07 total time elapsed so far: 5.000000 # loops : 50 mean,max change (kT/e) : 5.9035784E-07 2.6750565E-04 energy calculations done at 5.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.190000 DelPhi exited at 11:28:07 5.189u 0.229s 0:05.75 93.9% 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 Sat Oct 15 2011 at 11:28:07 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5009 !!! WARNING: GLM 203 has a net charge of -0.0940 !!! WARNING: FAD 4965 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: 0.7843137 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): -24.31100 75.55400 ymin,ymax (A): -25.78700 95.90200 zmin,zma (A): -23.58200 112.5880 x,y,z range (A): 99.86501 121.6890 136.1700 scale (grids/A): 0.7843137 object centre (A): 25.62150 35.05750 44.50300 number of atom coordinates read : 5009 total number of charged atoms : 4391 net assigned charge : 1.406037 assigned positive charge : 702.2128 centred at (gu) : 74.28325 72.57790 63.24761 assigned negative charge : -700.8102 centred at (gu) : 74.40651 72.70640 63.32514 start vw surface at 0.1800000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 22938 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51322 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 3.028480 m= 2079 mr = 12372 m= 19 mr = 612 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 179 time to turn everything in is 0.3500000 number of dielectric boundary points 12052 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2785 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 20251 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) : 0.2614379 object centre at (A) : 25.62150 35.05750 44.50300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8930840E-04 -7.3311030E-06 midg,1,midg; midg,igrid,midg -1.0964663E-05 -1.4577772E-06 1,midg,midg; igrid,midg,midg 1.6719416E-05 -3.4038430E-07 gauss-seidel spectral radius is 0.9916604 estimated iterations to convergence 89 setup time was (sec) 0.6900000 now iterating at: 11:28:08 rms-change max change #iterations 0.4661959 57.09177 at 10iterations 7.1881555E-02 6.528175 at 20iterations 1.1206665E-02 1.055854 at 30iterations 1.8957594E-03 0.1617298 at 40iterations 4.7637557E-04 3.7231445E-02 at 50iterations 1.8578071E-04 1.4348030E-02 at 60iterations 8.4024119E-05 6.2899590E-03 at 70iterations 3.8558224E-05 2.9163361E-03 at 80iterations 1.7770699E-05 1.3461113E-03 at 90iterations 8.1897579E-06 6.2179565E-04 at 100iterations 3.7801512E-06 2.8967857E-04 at 110iterations 1.7494411E-06 1.3399124E-04 at 120iterations finished qdiffx linear iterations at : 11:28:17 total time elapsed so far: 9.150000 # loops : 120 mean,max change (kT/e) : 1.7494411E-06 1.3399124E-04 energy calculations done at 9.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.330000 DelPhi exited at 11:28:17 9.332u 0.271s 0:09.90 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 Sat Oct 15 2011 at 11:28:17 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5009 !!! WARNING: GLM 203 has a net charge of -0.0940 !!! WARNING: FAD 4965 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: 1.176471 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): -24.31100 75.55400 ymin,ymax (A): -25.78700 95.90200 zmin,zma (A): -23.58200 112.5880 x,y,z range (A): 99.86501 121.6890 136.1700 scale (grids/A): 1.176471 object centre (A): 25.62150 35.05750 44.50300 number of atom coordinates read : 5009 total number of charged atoms : 4391 net assigned charge : 1.406037 assigned positive charge : 702.2128 centred at (gu) : 66.42461 63.86666 49.87133 assigned negative charge : -700.8102 centred at (gu) : 66.60955 64.05961 49.98754 start vw surface at 0.2100000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 55152 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51322 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.999360 m= 10423 mr = 32893 m= 368 mr = 5673 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 566 time to turn everything in is 0.6800000 number of dielectric boundary points 27334 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 918 ## 54 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 28778 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) : 0.7843137 object centre at (A) : 25.62150 35.05750 44.50300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5518830E-02 -4.7321344E-04 midg,1,midg; midg,igrid,midg 1.0433769E-03 -1.0104729E-04 1,midg,midg; igrid,midg,midg 1.7769722E-03 -2.7200638E-05 gauss-seidel spectral radius is 0.9962192 estimated iterations to convergence 130 setup time was (sec) 1.000000 now iterating at: 11:28:19 rms-change max change #iterations 2.096743 141.5234 at 10iterations 0.6210275 38.80231 at 20iterations 0.1804757 9.487339 at 30iterations 5.2174032E-02 3.432941 at 40iterations 1.5055628E-02 0.7284565 at 50iterations 4.4077239E-03 0.2363644 at 60iterations 1.3598037E-03 6.6017151E-02 at 70iterations 5.0457910E-04 2.5558472E-02 at 80iterations 2.3761025E-04 1.1434555E-02 at 90iterations 1.3309125E-04 6.5002441E-03 at 100iterations 7.9094665E-05 3.6869049E-03 at 110iterations 4.7494013E-05 2.2258759E-03 at 120iterations 2.8628567E-05 1.3580322E-03 at 130iterations 1.7280167E-05 8.1825256E-04 at 140iterations 1.0431881E-05 4.9877167E-04 at 150iterations 6.3058060E-06 3.0517578E-04 at 160iterations 3.8314406E-06 1.8882751E-04 at 170iterations 2.3420694E-06 1.2397766E-04 at 180iterations finished qdiffx linear iterations at : 11:28:32 total time elapsed so far: 13.93000 # loops : 180 mean,max change (kT/e) : 2.3420694E-06 1.2397766E-04 energy calculations done at 13.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.10000 DelPhi exited at 11:28:32 14.104u 0.312s 0:14.91 96.6% 0+0k 0+0io 0pf+0w