Sun Oct 9 12:02:49 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 Sun Oct 9 2011 at 12:02:49 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2397 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 0.6819924 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): -6.932000 44.66600 ymin,ymax (A): -13.74200 38.45800 zmin,zma (A): 0.5020000 45.00000 x,y,z range (A): 51.59800 52.20000 44.49800 scale (grids/A): 0.6819924 object centre (A): 18.86700 12.35800 22.75100 number of atom coordinates read : 2397 total number of charged atoms : 2252 net assigned charge : 5.406015 assigned positive charge : 368.0331 centred at (gu) : 89.76812 90.78433 91.21864 assigned negative charge : -362.6276 centred at (gu) : 89.80134 90.89001 91.34241 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7622 nv = 96 ne = 84 npr = 47653 no. pairs analyzed = 47653 no. exposed pairs = 2929 no. arc points = 20838 no. surface atoms = 985 nbur = 1412 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 529 mr = 4307 m= 2 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3758 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2028 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8658 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0256013E-08 -1.9309626E-08 midg,1,midg; midg,igrid,midg 5.0014769E-08 -1.0547809E-08 1,midg,midg; igrid,midg,midg 3.7481502E-08 1.4036986E-08 gauss-seidel spectral radius is 0.9888357 estimated iterations to convergence 77 setup time was (sec) 0.3800000 now iterating at: 12:02:49 rms-change max change #iterations 0.1890802 26.52798 at 10iterations 2.1752806E-02 2.974483 at 20iterations 2.5160688E-03 0.3314342 at 30iterations 3.2443230E-04 3.9218903E-02 at 40iterations 5.1379739E-05 6.7844391E-03 at 50iterations finished qdiffx linear iterations at : 12:02:52 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 5.1379739E-05 6.7844391E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 12:02:53 3.395u 0.179s 0:03.85 92.4% 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 Sun Oct 9 2011 at 12:02:53 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2397 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 2.045977 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): -6.932000 44.66600 ymin,ymax (A): -13.74200 38.45800 zmin,zma (A): 0.5020000 45.00000 x,y,z range (A): 51.59800 52.20000 44.49800 scale (grids/A): 2.045977 object centre (A): 18.86700 12.35800 22.75100 number of atom coordinates read : 2397 total number of charged atoms : 2252 net assigned charge : 5.406015 assigned positive charge : 368.0331 centred at (gu) : 89.30387 92.35250 93.65543 assigned negative charge : -362.6276 centred at (gu) : 89.40372 92.66974 94.02695 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20838 grid for indexing accessible points = 1.400000 m= 32211 mr = 55978 m= 6326 mr = 24455 m= 545 mr = 4150 m= 19 mr = 248 m= 0 mr = 4 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 580 time to turn everything in is 0.4100000 number of dielectric boundary points 34698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 17805 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) : 0.6819924 object centre at (A) : 18.86700 12.35800 22.75100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1972067E-02 2.3419200E-03 midg,1,midg; midg,igrid,midg 2.4525346E-02 -2.3943705E-02 1,midg,midg; igrid,midg,midg 4.4396732E-02 -2.3618374E-02 gauss-seidel spectral radius is 0.9987924 estimated iterations to convergence 228 setup time was (sec) 0.6300000 now iterating at: 12:02:53 rms-change max change #iterations 4.727109 240.8572 at 10iterations 2.313653 90.26749 at 20iterations 1.128565 32.98533 at 30iterations 0.5523888 16.04675 at 40iterations 0.2706629 8.245317 at 50iterations 0.1327082 3.897274 at 60iterations 6.5117583E-02 2.162579 at 70iterations 3.1952027E-02 0.9817810 at 80iterations 1.5706860E-02 0.4331179 at 90iterations 7.7154716E-03 0.2585011 at 100iterations 3.8185103E-03 0.1165113 at 110iterations 1.9009610E-03 5.5983543E-02 at 120iterations finished qdiffx linear iterations at : 12:03:01 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 1.9009610E-03 5.5983543E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 12:03:01 7.897u 0.195s 0:08.36 96.6% 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 Sun Oct 9 2011 at 12:03:01 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2397 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 3.068965 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): -6.932000 44.66600 ymin,ymax (A): -13.74200 38.45800 zmin,zma (A): 0.5020000 45.00000 x,y,z range (A): 51.59800 52.20000 44.49800 scale (grids/A): 3.068965 object centre (A): 18.86700 12.35800 22.75100 number of atom coordinates read : 2397 total number of charged atoms : 2252 net assigned charge : 5.406015 assigned positive charge : 368.0331 centred at (gu) : 88.95560 93.52859 95.48309 assigned negative charge : -362.6276 centred at (gu) : 89.10564 94.00463 96.04041 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 185598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20838 grid for indexing accessible points = 1.400000 m= 99529 mr = 135287 m= 41275 mr = 82383 m= 11827 mr = 34050 m= 2252 mr = 9091 m= 223 mr = 1596 m= 10 mr = 129 m= 0 mr = 4 time to grow re-entrant surface = 0.6299999 no. cavity mid-points inaccessible to solvent = 1990 time to turn everything in is 1.080000 number of dielectric boundary points 78174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 18016 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) : 2.045977 object centre at (A) : 18.86700 12.35800 22.75100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5579902 -0.1304660 midg,1,midg; midg,igrid,midg 0.5586202 -0.2381097 1,midg,midg; igrid,midg,midg 0.4540180 -0.4744813 gauss-seidel spectral radius is 0.9992901 estimated iterations to convergence 296 setup time was (sec) 1.310000 now iterating at: 12:03:03 rms-change max change #iterations 10.68252 410.5162 at 10iterations 6.302974 127.1624 at 20iterations 3.704840 95.25069 at 30iterations 2.175915 48.52141 at 40iterations 1.274038 25.65100 at 50iterations 0.7455438 13.63638 at 60iterations 0.4362603 7.209732 at 70iterations 0.2541449 4.270546 at 80iterations 0.1481890 2.462412 at 90iterations 8.6416438E-02 1.508366 at 100iterations 5.0538279E-02 0.9106445 at 110iterations 2.9421205E-02 0.5997918 at 120iterations 1.7248129E-02 0.2986641 at 130iterations 1.0100229E-02 0.1737647 at 140iterations 5.9869103E-03 0.1025715 at 150iterations 3.5758982E-03 6.6013336E-02 at 160iterations 2.1864537E-03 4.0039063E-02 at 170iterations 1.3704301E-03 2.7805328E-02 at 180iterations finished qdiffx linear iterations at : 12:03:14 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 1.3704301E-03 2.7805328E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 12:03:14 12.888u 0.208s 0:13.36 97.9% 0+0k 0+0io 0pf+0w