Tue Oct 11 02:36:33 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 02:36:33 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 !!! WARNING: FMN 398 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6686324 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): 20.54600 67.71900 ymin,ymax (A): 14.47000 67.71301 zmin,zma (A): -17.33000 30.31000 x,y,z range (A): 47.17300 53.24300 47.64000 scale (grids/A): 0.6686324 object centre (A): 44.13250 41.09150 6.490000 number of atom coordinates read : 2777 total number of charged atoms : 2642 net assigned charge : 5.500029 assigned positive charge : 427.5182 centred at (gu) : 90.65753 90.37632 90.21774 assigned negative charge : -422.0193 centred at (gu) : 90.46613 90.54497 90.26946 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8324 nv = 96 ne = 84 npr = 57107 no. pairs analyzed = 57107 no. exposed pairs = 3449 no. arc points = 23714 no. surface atoms = 1148 nbur = 1629 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 440 mr = 4706 m= 5 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.2100000 number of dielectric boundary points 4007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2293 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9796 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9963967E-08 3.7507939E-09 midg,1,midg; midg,igrid,midg 5.7279642E-08 -3.0828708E-08 1,midg,midg; igrid,midg,midg -3.0136402E-08 7.7672077E-08 gauss-seidel spectral radius is 0.9884204 estimated iterations to convergence 76 setup time was (sec) 0.3900000 now iterating at: 02:36:34 rms-change max change #iterations 0.1852859 23.68580 at 10iterations 2.0805161E-02 2.735580 at 20iterations 2.5625331E-03 0.3181314 at 30iterations 4.1749433E-04 6.9396973E-02 at 40iterations 9.3258735E-05 1.6738892E-02 at 50iterations finished qdiffx linear iterations at : 02:36:37 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 9.3258735E-05 1.6738892E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 02:36:37 3.352u 0.176s 0:04.28 82.2% 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 02:36:37 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 !!! WARNING: FMN 398 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.005897 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): 20.54600 67.71900 ymin,ymax (A): 14.47000 67.71301 zmin,zma (A): -17.33000 30.31000 x,y,z range (A): 47.17300 53.24300 47.64000 scale (grids/A): 2.005897 object centre (A): 44.13250 41.09150 6.490000 number of atom coordinates read : 2777 total number of charged atoms : 2642 net assigned charge : 5.500029 assigned positive charge : 427.5182 centred at (gu) : 91.97209 91.12830 90.65234 assigned negative charge : -422.0193 centred at (gu) : 91.39799 91.63448 90.80828 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 90323 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23714 grid for indexing accessible points = 1.400000 m= 33193 mr = 63926 m= 5536 mr = 24837 m= 419 mr = 3531 m= 5 mr = 166 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2412 time to turn everything in is 0.4300000 number of dielectric boundary points 37016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 20899 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) : 0.6686324 object centre at (A) : 44.13250 41.09150 6.490000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5233926E-02 -2.9043574E-02 midg,1,midg; midg,igrid,midg 8.0497965E-02 -2.3779145E-02 1,midg,midg; igrid,midg,midg -1.9651426E-02 7.0012376E-02 gauss-seidel spectral radius is 0.9987835 estimated iterations to convergence 227 setup time was (sec) 0.6400000 now iterating at: 02:36:38 rms-change max change #iterations 4.927736 241.5233 at 10iterations 2.402794 81.24992 at 20iterations 1.174953 37.04341 at 30iterations 0.5722186 17.40394 at 40iterations 0.2800743 8.879921 at 50iterations 0.1371006 3.956817 at 60iterations 6.7113712E-02 1.972099 at 70iterations 3.3054017E-02 0.8718166 at 80iterations 1.6359100E-02 0.5388184 at 90iterations 8.2042199E-03 0.2290154 at 100iterations 4.2431667E-03 0.1422062 at 110iterations 2.2761521E-03 8.5853577E-02 at 120iterations finished qdiffx linear iterations at : 02:36:45 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 2.2761521E-03 8.5853577E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 02:36:46 7.828u 0.201s 0:08.75 91.6% 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 Tue Oct 11 2011 at 02:36:46 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 !!! WARNING: FMN 398 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.008846 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): 20.54600 67.71900 ymin,ymax (A): 14.47000 67.71301 zmin,zma (A): -17.33000 30.31000 x,y,z range (A): 47.17300 53.24300 47.64000 scale (grids/A): 3.008846 object centre (A): 44.13250 41.09150 6.490000 number of atom coordinates read : 2777 total number of charged atoms : 2642 net assigned charge : 5.500029 assigned positive charge : 427.5182 centred at (gu) : 92.95784 91.69229 90.97831 assigned negative charge : -422.0193 centred at (gu) : 92.09692 92.45165 91.21227 start vw surface at 0.1000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 208555 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23714 grid for indexing accessible points = 1.400000 m= 106846 mr = 154183 m= 39813 mr = 88243 m= 10277 mr = 32372 m= 1688 mr = 7858 m= 122 mr = 1137 m= 3 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 8042 time to turn everything in is 1.140000 number of dielectric boundary points 83454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 21136 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) : 2.005897 object centre at (A) : 44.13250 41.09150 6.490000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2003674 -0.3376891 midg,1,midg; midg,igrid,midg 1.016719 -0.4613666 1,midg,midg; igrid,midg,midg -0.2214516 0.6568109 gauss-seidel spectral radius is 0.9992967 estimated iterations to convergence 297 setup time was (sec) 1.380000 now iterating at: 02:36:48 rms-change max change #iterations 11.27213 361.3845 at 10iterations 6.655036 137.9434 at 20iterations 3.928185 70.80540 at 30iterations 2.306137 47.52184 at 40iterations 1.357739 22.58018 at 50iterations 0.7981845 12.67420 at 60iterations 0.4664854 7.813499 at 70iterations 0.2732671 4.365555 at 80iterations 0.1599213 2.481289 at 90iterations 9.3547687E-02 1.519996 at 100iterations 5.4926362E-02 0.8849096 at 110iterations 3.2131266E-02 0.5548668 at 120iterations 1.8893391E-02 0.3634605 at 130iterations 1.1190262E-02 0.2063904 at 140iterations 6.7249360E-03 0.1317978 at 150iterations 4.1323593E-03 9.3128204E-02 at 160iterations 2.6465612E-03 5.8204651E-02 at 170iterations 1.7883059E-03 3.8661957E-02 at 180iterations finished qdiffx linear iterations at : 02:36:59 total time elapsed so far: 13.00000 # loops : 180 mean,max change (kT/e) : 1.7883059E-03 3.8661957E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.12000 DelPhi exited at 02:37:00 13.125u 0.219s 0:13.68 97.4% 0+0k 0+0io 0pf+0w