Tue Oct 11 07:03:40 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 Tue Oct 11 2011 at 07:03:40 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3608 !!! WARNING: UMP 1153 has a net charge of -0.1000 !!! WARNING: CME 1 has a net charge of -0.1350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5436941 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): -25.09600 31.45900 ymin,ymax (A): -24.17600 41.30200 zmin,zma (A): -16.19700 36.50000 x,y,z range (A): 56.55500 65.47800 52.69700 scale (grids/A): 0.5436941 object centre (A): 3.181500 8.563002 10.15150 number of atom coordinates read : 3608 total number of charged atoms : 3456 net assigned charge : 4.265022 assigned positive charge : 551.8486 centred at (gu) : 90.10639 89.33701 89.46455 assigned negative charge : -547.5860 centred at (gu) : 90.29617 89.41588 89.64541 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6764 nv = 96 ne = 84 npr = 73420 no. pairs analyzed = 73420 no. exposed pairs = 4226 no. arc points = 29927 no. surface atoms = 1433 nbur = 2175 mkacc time = 0.1200000 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 = 1.596000 m= 233 mr = 3649 m= 0 mr = 8 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2700000 number of dielectric boundary points 3340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3082 ## 445 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 9005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7887600E-09 -1.0083691E-09 midg,1,midg; midg,igrid,midg 9.6991259E-10 -3.0615319E-10 1,midg,midg; igrid,midg,midg 1.5843803E-09 -1.2597668E-09 gauss-seidel spectral radius is 0.9826045 estimated iterations to convergence 62 setup time was (sec) 0.4600000 now iterating at: 07:03:41 rms-change max change #iterations 8.1843682E-02 12.94427 at 10iterations 6.1674230E-03 1.107941 at 20iterations 1.5185538E-03 0.2588971 at 30iterations 6.8637246E-04 0.1202619 at 40iterations 3.2045599E-04 5.6447983E-02 at 50iterations finished qdiffx linear iterations at : 07:03:44 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 3.2045599E-04 5.6447983E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 07:03:44 3.514u 0.152s 0:04.24 86.3% 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 Tue Oct 11 2011 at 07:03:45 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3608 !!! WARNING: UMP 1153 has a net charge of -0.1000 !!! WARNING: CME 1 has a net charge of -0.1350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.631082 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): -25.09600 31.45900 ymin,ymax (A): -24.17600 41.30200 zmin,zma (A): -16.19700 36.50000 x,y,z range (A): 56.55500 65.47800 52.69700 scale (grids/A): 1.631082 object centre (A): 3.181500 8.563002 10.15150 number of atom coordinates read : 3608 total number of charged atoms : 3456 net assigned charge : 4.265022 assigned positive charge : 551.8486 centred at (gu) : 90.31815 88.01042 88.39265 assigned negative charge : -547.5860 centred at (gu) : 90.88803 88.24747 88.93591 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 75509 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29927 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22670 mr = 52120 m= 2337 mr = 15984 m= 56 mr = 1186 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 833 time to turn everything in is 0.3800000 number of dielectric boundary points 31281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 378 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 26423 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) : 0.5436941 object centre at (A) : 3.181500 8.563002 10.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0538061E-02 -1.4434513E-02 midg,1,midg; midg,igrid,midg 2.2252381E-02 -8.6517632E-04 1,midg,midg; igrid,midg,midg 2.0317473E-02 -1.9524014E-02 gauss-seidel spectral radius is 0.9982446 estimated iterations to convergence 190 setup time was (sec) 0.6100000 now iterating at: 07:03:45 rms-change max change #iterations 3.745875 160.1080 at 10iterations 1.594768 54.35913 at 20iterations 0.6772189 25.69502 at 30iterations 0.2862706 9.647532 at 40iterations 0.1219579 4.077400 at 50iterations 5.2002773E-02 1.687592 at 60iterations 2.2427307E-02 0.8612595 at 70iterations 9.9722156E-03 0.3381515 at 80iterations 4.8703966E-03 0.1879044 at 90iterations 2.7269719E-03 0.1007938 at 100iterations 1.7772109E-03 6.6643000E-02 at 110iterations 1.2904661E-03 4.5350552E-02 at 120iterations finished qdiffx linear iterations at : 07:03:52 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 1.2904661E-03 4.5350552E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 07:03:53 7.830u 0.184s 0:08.45 94.7% 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 Tue Oct 11 2011 at 07:03:53 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3608 !!! WARNING: UMP 1153 has a net charge of -0.1000 !!! WARNING: CME 1 has a net charge of -0.1350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.446623 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): -25.09600 31.45900 ymin,ymax (A): -24.17600 41.30200 zmin,zma (A): -16.19700 36.50000 x,y,z range (A): 56.55500 65.47800 52.69700 scale (grids/A): 2.446623 object centre (A): 3.181500 8.563002 10.15150 number of atom coordinates read : 3608 total number of charged atoms : 3456 net assigned charge : 4.265022 assigned positive charge : 551.8486 centred at (gu) : 90.47674 87.01519 87.58857 assigned negative charge : -547.5860 centred at (gu) : 91.33189 87.37122 88.40385 start vw surface at 0.1100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 175378 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29927 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 79491 mr = 127166 m= 22423 mr = 63672 m= 3610 mr = 17250 m= 260 mr = 2425 m= 6 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 2658 time to turn everything in is 0.9000000 number of dielectric boundary points 70539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 27608 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) : 1.631082 object centre at (A) : 3.181500 8.563002 10.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1113400 -0.2292194 midg,1,midg; midg,igrid,midg 0.2596838 6.0410708E-02 1,midg,midg; igrid,midg,midg 0.3643377 -0.3447614 gauss-seidel spectral radius is 0.9991641 estimated iterations to convergence 273 setup time was (sec) 1.130000 now iterating at: 07:03:54 rms-change max change #iterations 9.563066 286.3181 at 10iterations 5.374425 129.7514 at 20iterations 3.019731 65.74096 at 30iterations 1.690153 34.23965 at 40iterations 0.9444015 19.62004 at 50iterations 0.5255050 9.907256 at 60iterations 0.2931879 5.748407 at 70iterations 0.1627070 3.148325 at 80iterations 9.0575069E-02 1.764295 at 90iterations 5.0360516E-02 0.9476089 at 100iterations 2.8072473E-02 0.5359697 at 110iterations 1.5672550E-02 0.3061762 at 120iterations 8.8418610E-03 0.2028732 at 130iterations 5.0629554E-03 0.1154327 at 140iterations 3.0095752E-03 7.2395325E-02 at 150iterations 1.9008394E-03 4.2613983E-02 at 160iterations 1.2988222E-03 2.7856827E-02 at 170iterations 9.6581923E-04 2.1492004E-02 at 180iterations finished qdiffx linear iterations at : 07:04:06 total time elapsed so far: 12.42000 # loops : 180 mean,max change (kT/e) : 9.6581923E-04 2.1492004E-02 energy calculations done at 12.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 07:04:06 12.549u 0.216s 0:13.23 96.3% 0+0k 0+0io 0pf+0w