Tue Oct 11 08:34:21 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 08:34:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2071 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: 0.7076409 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): 0.2689999 46.95500 ymin,ymax (A): 0.6079999 41.14400 zmin,zma (A): -3.280000 47.02800 x,y,z range (A): 46.68600 40.53600 50.30800 scale (grids/A): 0.7076409 object centre (A): 23.61200 20.87600 21.87400 number of atom coordinates read : 2071 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 90.92263 90.30302 90.76011 assigned negative charge : -312.6442 centred at (gu) : 91.06557 90.27589 90.83199 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7003 nv = 96 ne = 84 npr = 41502 no. pairs analyzed = 41502 no. exposed pairs = 2510 no. arc points = 17014 no. surface atoms = 854 nbur = 1217 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 4049 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1626 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7822 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.9157751E-08 2.2851184E-08 midg,1,midg; midg,igrid,midg 4.0275616E-08 7.3679075E-08 1,midg,midg; igrid,midg,midg 1.0552492E-07 -1.9951921E-08 gauss-seidel spectral radius is 0.9895877 estimated iterations to convergence 80 setup time was (sec) 0.3600000 now iterating at: 08:34:21 rms-change max change #iterations 0.1932140 25.47423 at 10iterations 2.4403971E-02 3.887645 at 20iterations 3.1924313E-03 0.4454727 at 30iterations 4.9291953E-04 8.3660126E-02 at 40iterations 1.1148051E-04 1.7333984E-02 at 50iterations finished qdiffx linear iterations at : 08:34:24 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.1148051E-04 1.7333984E-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) 3.360000 DelPhi exited at 08:34:25 3.363u 0.179s 0:04.09 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 08:34:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2071 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: 2.122923 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): 0.2689999 46.95500 ymin,ymax (A): 0.6079999 41.14400 zmin,zma (A): -3.280000 47.02800 x,y,z range (A): 46.68600 40.53600 50.30800 scale (grids/A): 2.122923 object centre (A): 23.61200 20.87600 21.87400 number of atom coordinates read : 2071 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 92.76786 90.90902 92.28045 assigned negative charge : -312.6442 centred at (gu) : 93.19675 90.82784 92.49617 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74638 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17014 grid for indexing accessible points = 1.400000 m= 29709 mr = 53236 m= 5632 mr = 22594 m= 458 mr = 3727 m= 9 mr = 235 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 30654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15623 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) : 0.7076409 object centre at (A) : 23.61200 20.87600 21.87400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8029870E-02 6.7333981E-02 midg,1,midg; midg,igrid,midg 2.1551235E-03 3.3121604E-02 1,midg,midg; igrid,midg,midg 2.8396541E-02 1.2123281E-02 gauss-seidel spectral radius is 0.9988278 estimated iterations to convergence 231 setup time was (sec) 0.6000000 now iterating at: 08:34:26 rms-change max change #iterations 4.616491 182.2940 at 10iterations 2.282617 74.05792 at 20iterations 1.129516 36.36787 at 30iterations 0.5620463 17.34799 at 40iterations 0.2796443 8.388241 at 50iterations 0.1383949 4.307745 at 60iterations 6.8730995E-02 2.203153 at 70iterations 3.4118950E-02 0.9949751 at 80iterations 1.7044969E-02 0.4896049 at 90iterations 8.4818266E-03 0.2919680 at 100iterations 4.2438759E-03 0.1327667 at 110iterations 2.1496925E-03 7.1403503E-02 at 120iterations finished qdiffx linear iterations at : 08:34:33 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 2.1496925E-03 7.1403503E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 08:34:34 7.874u 0.203s 0:08.73 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 Tue Oct 11 2011 at 08:34:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2071 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.184384 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): 0.2689999 46.95500 ymin,ymax (A): 0.6079999 41.14400 zmin,zma (A): -3.280000 47.02800 x,y,z range (A): 46.68600 40.53600 50.30800 scale (grids/A): 3.184384 object centre (A): 23.61200 20.87600 21.87400 number of atom coordinates read : 2071 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 94.15182 91.36346 93.42061 assigned negative charge : -312.6442 centred at (gu) : 94.79516 91.24194 93.74429 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 172036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17014 grid for indexing accessible points = 1.400000 m= 93504 mr = 128289 m= 37296 mr = 77989 m= 10593 mr = 30630 m= 1968 mr = 8175 m= 213 mr = 1404 m= 3 mr = 128 m= 0 mr = 2 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.140000 number of dielectric boundary points 68996 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 15752 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) : 2.122923 object centre at (A) : 23.61200 20.87600 21.87400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3646536 0.7012776 midg,1,midg; midg,igrid,midg -2.6607044E-02 0.2559075 1,midg,midg; igrid,midg,midg 0.2399912 0.3358901 gauss-seidel spectral radius is 0.9992937 estimated iterations to convergence 297 setup time was (sec) 1.370000 now iterating at: 08:34:35 rms-change max change #iterations 10.29407 372.7419 at 10iterations 6.088803 129.4310 at 20iterations 3.582124 70.47535 at 30iterations 2.109836 39.47848 at 40iterations 1.236491 23.64674 at 50iterations 0.7270267 15.51006 at 60iterations 0.4252807 7.711612 at 70iterations 0.2493502 4.539907 at 80iterations 0.1456562 2.587061 at 90iterations 8.5319214E-02 1.543177 at 100iterations 4.9894314E-02 0.8592606 at 110iterations 2.9236270E-02 0.5756454 at 120iterations 1.7199403E-02 0.3300896 at 130iterations 1.0194390E-02 0.1738091 at 140iterations 6.1142882E-03 0.1071701 at 150iterations 3.7458953E-03 7.9067230E-02 at 160iterations 2.3856501E-03 4.3475151E-02 at 170iterations 1.5990895E-03 2.9373169E-02 at 180iterations finished qdiffx linear iterations at : 08:34:46 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 1.5990895E-03 2.9373169E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 08:34:47 12.693u 0.212s 0:13.28 97.1% 0+0k 0+0io 0pf+0w