Sat Oct 15 15:45:22 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 Sat Oct 15 2011 at 15:45:22 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2732 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6618084 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): -8.577000 38.47800 ymin,ymax (A): -26.40700 21.61600 zmin,zma (A): -9.814000 43.97800 x,y,z range (A): 47.05500 48.02300 53.79200 scale (grids/A): 0.6618084 object centre (A): 14.95050 -2.395500 17.08200 number of atom coordinates read : 2732 total number of charged atoms : 2581 net assigned charge : 4.162025 assigned positive charge : 409.4446 centred at (gu) : 90.36145 90.10480 89.06681 assigned negative charge : -405.2834 centred at (gu) : 90.63867 89.91854 89.10436 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7942 nv = 96 ne = 84 npr = 56822 no. pairs analyzed = 56822 no. exposed pairs = 3306 no. arc points = 22551 no. surface atoms = 1110 nbur = 1622 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 467 mr = 4616 m= 6 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.2100000 number of dielectric boundary points 3734 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2222 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9483 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3562453E-08 2.7262961E-09 midg,1,midg; midg,igrid,midg -2.9066429E-08 5.1967348E-08 1,midg,midg; igrid,midg,midg 6.4498565E-08 -5.4474203E-08 gauss-seidel spectral radius is 0.9881719 estimated iterations to convergence 75 setup time was (sec) 0.3900000 now iterating at: 15:45:23 rms-change max change #iterations 0.1733806 21.29539 at 10iterations 1.9005854E-02 2.514609 at 20iterations 2.0553749E-03 0.2639313 at 30iterations 2.3636516E-04 3.0750275E-02 at 40iterations 3.2666976E-05 4.0073395E-03 at 50iterations finished qdiffx linear iterations at : 15:45:27 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 3.2666976E-05 4.0073395E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 15:45:28 3.427u 0.179s 0:05.31 67.6% 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 15:45:28 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2732 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.985425 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): -8.577000 38.47800 ymin,ymax (A): -26.40700 21.61600 zmin,zma (A): -9.814000 43.97800 x,y,z range (A): 47.05500 48.02300 53.79200 scale (grids/A): 1.985425 object centre (A): 14.95050 -2.395500 17.08200 number of atom coordinates read : 2732 total number of charged atoms : 2581 net assigned charge : 4.162025 assigned positive charge : 409.4446 centred at (gu) : 91.08380 90.31400 87.19981 assigned negative charge : -405.2834 centred at (gu) : 91.91558 89.75536 87.31287 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 85279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22551 grid for indexing accessible points = 1.400000 m= 32306 mr = 60906 m= 5437 mr = 24368 m= 347 mr = 3525 m= 1 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1950 time to turn everything in is 0.4300000 number of dielectric boundary points 34426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20395 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) : 0.6618084 object centre at (A) : 14.95050 -2.395500 17.08200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0504844E-03 -1.0345774E-02 midg,1,midg; midg,igrid,midg -2.0091100E-02 4.2133532E-02 1,midg,midg; igrid,midg,midg 6.6492260E-02 -1.5506344E-03 gauss-seidel spectral radius is 0.9987490 estimated iterations to convergence 224 setup time was (sec) 0.6500000 now iterating at: 15:45:28 rms-change max change #iterations 4.730684 224.2316 at 10iterations 2.303536 67.42744 at 20iterations 1.112149 34.55339 at 30iterations 0.5399354 17.72581 at 40iterations 0.2618364 7.540558 at 50iterations 0.1270443 3.614341 at 60iterations 6.1382186E-02 1.765740 at 70iterations 2.9800350E-02 0.9169922 at 80iterations 1.4418921E-02 0.4258118 at 90iterations 6.9999541E-03 0.2026367 at 100iterations 3.3970606E-03 0.1163387 at 110iterations 1.6544599E-03 4.9025536E-02 at 120iterations finished qdiffx linear iterations at : 15:45:36 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.6544599E-03 4.9025536E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 15:45:36 8.021u 0.224s 0:08.67 95.0% 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 Sat Oct 15 2011 at 15:45:36 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2732 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.978138 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): -8.577000 38.47800 ymin,ymax (A): -26.40700 21.61600 zmin,zma (A): -9.814000 43.97800 x,y,z range (A): 47.05500 48.02300 53.79200 scale (grids/A): 2.978138 object centre (A): 14.95050 -2.395500 17.08200 number of atom coordinates read : 2732 total number of charged atoms : 2581 net assigned charge : 4.162025 assigned positive charge : 409.4446 centred at (gu) : 91.62540 90.47099 85.79961 assigned negative charge : -405.2834 centred at (gu) : 92.87334 89.63287 85.96924 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 197195 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22551 grid for indexing accessible points = 1.400000 m= 103511 mr = 146836 m= 38909 mr = 86133 m= 9652 mr = 31688 m= 1471 mr = 7374 m= 102 mr = 1069 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.6299999 no. cavity mid-points inaccessible to solvent = 6380 time to turn everything in is 1.090000 number of dielectric boundary points 77679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 20636 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) : 1.985425 object centre at (A) : 14.95050 -2.395500 17.08200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3337587 -0.1261311 midg,1,midg; midg,igrid,midg -0.2149123 0.4357249 1,midg,midg; igrid,midg,midg 0.5869905 7.8750864E-02 gauss-seidel spectral radius is 0.9992855 estimated iterations to convergence 295 setup time was (sec) 1.320000 now iterating at: 15:45:38 rms-change max change #iterations 10.78826 345.6586 at 10iterations 6.362921 174.5919 at 20iterations 3.739352 71.04976 at 30iterations 2.193339 42.16599 at 40iterations 1.284999 25.57093 at 50iterations 0.7510440 13.65598 at 60iterations 0.4381740 7.428878 at 70iterations 0.2557332 4.304139 at 80iterations 0.1490249 2.694429 at 90iterations 8.6627215E-02 1.445311 at 100iterations 5.0614398E-02 0.9328403 at 110iterations 2.9467084E-02 0.5278091 at 120iterations 1.7176881E-02 0.2944040 at 130iterations 1.0002394E-02 0.1677037 at 140iterations 5.8593424E-03 0.1014504 at 150iterations 3.4372674E-03 5.5166245E-02 at 160iterations 2.0322034E-03 3.5804749E-02 at 170iterations 1.2147879E-03 2.0974159E-02 at 180iterations finished qdiffx linear iterations at : 15:45:49 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 1.2147879E-03 2.0974159E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.85000 DelPhi exited at 15:45:50 12.849u 0.214s 0:13.36 97.6% 0+0k 0+0io 0pf+0w