Tue Oct 11 06:01:42 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 Tue Oct 11 2011 at 06:01:42 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7123134 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): 25.79300 72.22800 ymin,ymax (A): -18.48600 31.49200 zmin,zma (A): 4.305000 46.54200 x,y,z range (A): 46.43500 49.97800 42.23700 scale (grids/A): 0.7123134 object centre (A): 49.01050 6.503000 25.42350 number of atom coordinates read : 2327 total number of charged atoms : 2000 net assigned charge : 6.039011 assigned positive charge : 327.3059 centred at (gu) : 89.23201 90.11051 90.21774 assigned negative charge : -321.2671 centred at (gu) : 89.35987 90.04960 90.29852 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7276 nv = 96 ne = 84 npr = 42789 no. pairs analyzed = 42789 no. exposed pairs = 2565 no. arc points = 17596 no. surface atoms = 875 nbur = 1452 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 507 mr = 4231 m= 2 mr = 95 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 0.2800000 number of dielectric boundary points 3459 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1641 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8102 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7920804E-08 1.0752334E-08 midg,1,midg; midg,igrid,midg 2.1474465E-08 9.2923393E-08 1,midg,midg; igrid,midg,midg 1.4887166E-07 -1.3997130E-08 gauss-seidel spectral radius is 0.9897281 estimated iterations to convergence 80 setup time was (sec) 0.5200000 now iterating at: 06:01:42 rms-change max change #iterations 0.2093334 29.35027 at 10iterations 2.7057376E-02 4.135132 at 20iterations 3.6562134E-03 0.5133972 at 30iterations 6.0854026E-04 7.3322296E-02 at 40iterations 1.5026031E-04 1.9565582E-02 at 50iterations finished qdiffx linear iterations at : 06:01:45 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.5026031E-04 1.9565582E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 06:01:46 3.470u 0.192s 0:04.10 89.2% 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 06:01:46 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.136940 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): 25.79300 72.22800 ymin,ymax (A): -18.48600 31.49200 zmin,zma (A): 4.305000 46.54200 x,y,z range (A): 46.43500 49.97800 42.23700 scale (grids/A): 2.136940 object centre (A): 49.01050 6.503000 25.42350 number of atom coordinates read : 2327 total number of charged atoms : 2000 net assigned charge : 6.039011 assigned positive charge : 327.3059 centred at (gu) : 87.69595 90.33135 90.65318 assigned negative charge : -321.2671 centred at (gu) : 88.07954 90.14895 90.89562 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 77030 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17596 grid for indexing accessible points = 1.400000 m= 31721 mr = 54904 m= 6300 mr = 24214 m= 616 mr = 4256 m= 18 mr = 330 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 31979 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 15885 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) : 0.7123134 object centre at (A) : 49.01050 6.503000 25.42350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0396812E-02 2.8736496E-02 midg,1,midg; midg,igrid,midg 4.6770487E-02 2.6540088E-02 1,midg,midg; igrid,midg,midg 4.4398006E-02 -4.9223054E-02 gauss-seidel spectral radius is 0.9988480 estimated iterations to convergence 233 setup time was (sec) 0.9900000 now iterating at: 06:01:47 rms-change max change #iterations 4.706532 208.3689 at 10iterations 2.339079 74.12952 at 20iterations 1.167013 39.54414 at 30iterations 0.5816718 16.38022 at 40iterations 0.2916182 8.872388 at 50iterations 0.1453530 4.894371 at 60iterations 7.2361283E-02 2.040825 at 70iterations 3.6315687E-02 1.083023 at 80iterations 1.8165536E-02 0.5243802 at 90iterations 9.1697769E-03 0.2829342 at 100iterations 4.6308916E-03 0.1393814 at 110iterations 2.3936520E-03 7.7547073E-02 at 120iterations finished qdiffx linear iterations at : 06:01:54 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 2.3936520E-03 7.7547073E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 06:01:54 7.828u 0.185s 0:08.33 96.0% 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 06:01:54 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.205410 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): 25.79300 72.22800 ymin,ymax (A): -18.48600 31.49200 zmin,zma (A): 4.305000 46.54200 x,y,z range (A): 46.43500 49.97800 42.23700 scale (grids/A): 3.205410 object centre (A): 49.01050 6.503000 25.42350 number of atom coordinates read : 2327 total number of charged atoms : 2000 net assigned charge : 6.039011 assigned positive charge : 327.3059 centred at (gu) : 86.54388 90.49693 90.97976 assigned negative charge : -321.2671 centred at (gu) : 87.11934 90.22351 91.34343 start vw surface at 0.1500000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 177886 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17596 grid for indexing accessible points = 1.400000 m= 97951 mr = 132381 m= 40760 mr = 81860 m= 11951 mr = 33658 m= 2520 mr = 9463 m= 293 mr = 1809 m= 20 mr = 205 m= 0 mr = 7 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.960000 number of dielectric boundary points 71998 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 16000 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) : 2.136940 object centre at (A) : 49.01050 6.503000 25.42350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1016255 0.2310934 midg,1,midg; midg,igrid,midg 0.3548302 0.1188874 1,midg,midg; igrid,midg,midg 0.4315403 -0.6121543 gauss-seidel spectral radius is 0.9993008 estimated iterations to convergence 298 setup time was (sec) 2.280000 now iterating at: 06:01:57 rms-change max change #iterations 10.50636 375.4196 at 10iterations 6.212133 123.7193 at 20iterations 3.676453 72.91168 at 30iterations 2.170311 39.46749 at 40iterations 1.278732 27.59800 at 50iterations 0.7509189 15.17063 at 60iterations 0.4415052 7.447282 at 70iterations 0.2596101 4.535980 at 80iterations 0.1523500 2.686445 at 90iterations 8.9471526E-02 1.543493 at 100iterations 5.2523918E-02 0.9847870 at 110iterations 3.1048972E-02 0.5448151 at 120iterations 1.8427992E-02 0.3120613 at 130iterations 1.1110280E-02 0.2098808 at 140iterations 6.8513709E-03 0.1195526 at 150iterations 4.3557594E-03 7.9788208E-02 at 160iterations 2.9150546E-03 5.7453156E-02 at 170iterations 2.0663263E-03 3.8501740E-02 at 180iterations finished qdiffx linear iterations at : 06:02:09 total time elapsed so far: 14.28000 # loops : 180 mean,max change (kT/e) : 2.0663263E-03 3.8501740E-02 energy calculations done at 14.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.51000 DelPhi exited at 06:02:10 14.510u 0.225s 0:15.80 93.2% 0+0k 0+0io 0pf+0w