Mon Oct 10 20:16:29 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 20:16:29 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6116523 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): -11.83900 45.29700 ymin,ymax (A): 30.16200 82.62000 zmin,zma (A): -12.82900 45.37400 x,y,z range (A): 57.13600 52.45800 58.20300 scale (grids/A): 0.6116523 object centre (A): 16.72900 56.39100 16.27250 number of atom coordinates read : 2589 total number of charged atoms : 2451 net assigned charge : -2.999988 assigned positive charge : 382.5349 centred at (gu) : 89.59312 90.57324 90.61787 assigned negative charge : -385.5359 centred at (gu) : 89.62231 90.67669 90.59025 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6593 nv = 96 ne = 84 npr = 51888 no. pairs analyzed = 51888 no. exposed pairs = 3606 no. arc points = 26116 no. surface atoms = 1208 nbur = 1381 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 297 mr = 3146 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2596 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7971 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8587976E-09 -4.6994758E-10 midg,1,midg; midg,igrid,midg 3.0065084E-09 -8.2476541E-09 1,midg,midg; igrid,midg,midg -3.6482051E-10 -3.0683232E-09 gauss-seidel spectral radius is 0.9861744 estimated iterations to convergence 70 setup time was (sec) 0.5100000 now iterating at: 20:16:30 rms-change max change #iterations 0.1122474 20.31627 at 10iterations 9.8271742E-03 1.572689 at 20iterations 8.7965361E-04 0.1485276 at 30iterations 8.1132530E-05 1.3847351E-02 at 40iterations 8.3705745E-06 1.3084412E-03 at 50iterations finished qdiffx linear iterations at : 20:16:32 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 8.3705745E-06 1.3084412E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 20:16:33 3.081u 0.138s 0:03.57 89.9% 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 20:16:33 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 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: 1.834957 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): -11.83900 45.29700 ymin,ymax (A): 30.16200 82.62000 zmin,zma (A): -12.82900 45.37400 x,y,z range (A): 57.13600 52.45800 58.20300 scale (grids/A): 1.834957 object centre (A): 16.72900 56.39100 16.27250 number of atom coordinates read : 2589 total number of charged atoms : 2451 net assigned charge : -2.999988 assigned positive charge : 382.5349 centred at (gu) : 88.77897 91.71936 91.85317 assigned negative charge : -385.5359 centred at (gu) : 88.86681 92.02988 91.77058 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26116 grid for indexing accessible points = 1.400000 m= 23445 mr = 45002 m= 3544 mr = 15933 m= 159 mr = 1906 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 34284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19221 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) : 0.6116523 object centre at (A) : 16.72900 56.39100 16.27250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3500319E-02 -3.7641659E-02 midg,1,midg; midg,igrid,midg 1.3919946E-02 -1.9777562E-02 1,midg,midg; igrid,midg,midg 1.5249419E-02 -2.1817249E-03 gauss-seidel spectral radius is 0.9985542 estimated iterations to convergence 209 setup time was (sec) 0.7600000 now iterating at: 20:16:34 rms-change max change #iterations 3.931572 177.6952 at 10iterations 1.781842 61.08188 at 20iterations 0.8162147 30.85146 at 30iterations 0.3727956 13.03242 at 40iterations 0.1702166 5.609196 at 50iterations 7.7734783E-02 2.656597 at 60iterations 3.5413165E-02 1.233850 at 70iterations 1.6221199E-02 0.5345688 at 80iterations 7.4384874E-03 0.2692766 at 90iterations 3.3971223E-03 0.1197815 at 100iterations 1.5539727E-03 5.3136826E-02 at 110iterations 7.1405375E-04 2.4230957E-02 at 120iterations finished qdiffx linear iterations at : 20:16:40 total time elapsed so far: 6.800000 # loops : 120 mean,max change (kT/e) : 7.1405375E-04 2.4230957E-02 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.980000 DelPhi exited at 20:16:40 6.978u 0.180s 0:07.78 91.9% 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 20:16:41 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.752435 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): -11.83900 45.29700 ymin,ymax (A): 30.16200 82.62000 zmin,zma (A): -12.82900 45.37400 x,y,z range (A): 57.13600 52.45800 58.20300 scale (grids/A): 2.752435 object centre (A): 16.72900 56.39100 16.27250 number of atom coordinates read : 2589 total number of charged atoms : 2451 net assigned charge : -2.999988 assigned positive charge : 382.5349 centred at (gu) : 88.16821 92.57907 92.77962 assigned negative charge : -385.5359 centred at (gu) : 88.30019 93.04473 92.65598 start vw surface at 0.1700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 161903 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26116 grid for indexing accessible points = 1.400000 m= 75854 mr = 110073 m= 26361 mr = 58957 m= 6139 mr = 20056 m= 667 mr = 4227 m= 11 mr = 287 m= 0 mr = 3 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 77332 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 19606 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) : 1.834957 object centre at (A) : 16.72900 56.39100 16.27250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1145527 -0.3839410 midg,1,midg; midg,igrid,midg 0.1992847 -0.1320182 1,midg,midg; igrid,midg,midg 0.1876787 -6.7206666E-02 gauss-seidel spectral radius is 0.9992499 estimated iterations to convergence 288 setup time was (sec) 1.510000 now iterating at: 20:16:42 rms-change max change #iterations 9.629169 365.9577 at 10iterations 5.688879 149.3880 at 20iterations 3.324343 83.03027 at 30iterations 1.930372 43.70749 at 40iterations 1.116665 24.92795 at 50iterations 0.6463945 13.46977 at 60iterations 0.3722097 7.131019 at 70iterations 0.2140087 4.358414 at 80iterations 0.1226714 2.407679 at 90iterations 7.0407152E-02 1.509817 at 100iterations 4.0334988E-02 0.8093052 at 110iterations 2.3135943E-02 0.4702721 at 120iterations 1.3263918E-02 0.2677917 at 130iterations 7.5898343E-03 0.1383219 at 140iterations 4.3458622E-03 8.4848404E-02 at 150iterations 2.4868408E-03 4.7063828E-02 at 160iterations 1.4267908E-03 2.7818680E-02 at 170iterations 8.1790512E-04 1.6021729E-02 at 180iterations finished qdiffx linear iterations at : 20:16:52 total time elapsed so far: 10.88000 # loops : 180 mean,max change (kT/e) : 8.1790512E-04 1.6021729E-02 energy calculations done at 10.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.04000 DelPhi exited at 20:16:52 11.045u 0.175s 0:11.76 95.3% 0+0k 0+0io 0pf+0w