Tue Nov 22 14:21:44 PST 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 Nov 22 2011 at 14:21:49 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 0.6434937 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): -6.129000 34.89800 ymin,ymax (A): -4.037000 49.53700 zmin,zma (A): -24.42000 30.90300 x,y,z range (A): 41.02700 53.57400 55.32300 scale (grids/A): 0.6434937 object centre (A): 14.38450 22.75000 3.241500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 290.6260 centred at (gu) : 90.89274 92.55505 90.23594 assigned negative charge : -285.6263 centred at (gu) : 90.95782 92.64186 90.19382 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5580 nv = 96 ne = 84 npr = 40320 no. pairs analyzed = 40320 no. exposed pairs = 2400 no. arc points = 17080 no. surface atoms = 817 nbur = 1145 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 299 mr = 3147 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.2200000 number of dielectric boundary points 2689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1732 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6580 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1185348E-09 1.2808778E-08 midg,1,midg; midg,igrid,midg 9.5851487E-09 -3.0616773E-10 1,midg,midg; igrid,midg,midg 1.1872899E-08 2.4962101E-09 gauss-seidel spectral radius is 0.9874300 estimated iterations to convergence 73 setup time was (sec) 0.4300000 now iterating at: 14:21:52 rms-change max change #iterations 0.1272184 21.21979 at 10iterations 1.2947762E-02 2.065231 at 20iterations 1.2852731E-03 0.2004128 at 30iterations 1.2945378E-04 1.9394875E-02 at 40iterations 1.3021381E-05 1.9950867E-03 at 50iterations finished qdiffx linear iterations at : 14:22:00 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 1.3021381E-05 1.9950867E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 14:22:01 3.114u 0.162s 0:13.60 24.0% 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 Nov 22 2011 at 14:22:04 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 1.930481 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): -6.129000 34.89800 ymin,ymax (A): -4.037000 49.53700 zmin,zma (A): -24.42000 30.90300 x,y,z range (A): 41.02700 53.57400 55.32300 scale (grids/A): 1.930481 object centre (A): 14.38450 22.75000 3.241500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 290.6260 centred at (gu) : 92.67828 97.66538 90.70786 assigned negative charge : -285.6263 centred at (gu) : 92.87370 97.92579 90.58159 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 60004 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17080 grid for indexing accessible points = 1.400000 m= 22633 mr = 41877 m= 3396 mr = 17383 m= 174 mr = 2204 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1519 time to turn everything in is 0.4000000 number of dielectric boundary points 24680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 14446 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) : 0.6434937 object centre at (A) : 14.38450 22.75000 3.241500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6990365E-02 2.0979006E-02 midg,1,midg; midg,igrid,midg 2.6217107E-02 4.8695905E-03 1,midg,midg; igrid,midg,midg 1.0015295E-02 8.4026274E-04 gauss-seidel spectral radius is 0.9985915 estimated iterations to convergence 211 setup time was (sec) 0.6600000 now iterating at: 14:22:08 rms-change max change #iterations 3.678051 156.9268 at 10iterations 1.711109 57.50797 at 20iterations 0.7894922 29.12882 at 30iterations 0.3672834 12.39684 at 40iterations 0.1696054 5.741718 at 50iterations 7.8468047E-02 2.764545 at 60iterations 3.6243849E-02 1.371997 at 70iterations 1.6724046E-02 0.6025162 at 80iterations 7.7367360E-03 0.2858133 at 90iterations 3.5774917E-03 0.1228113 at 100iterations 1.6600947E-03 5.7102203E-02 at 110iterations 7.7068951E-04 2.7992249E-02 at 120iterations finished qdiffx linear iterations at : 14:22:30 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 7.7068951E-04 2.7992249E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 14:22:31 7.084u 0.181s 0:27.70 26.2% 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 Nov 22 2011 at 14:22:33 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 2.895722 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): -6.129000 34.89800 ymin,ymax (A): -4.037000 49.53700 zmin,zma (A): -24.42000 30.90300 x,y,z range (A): 41.02700 53.57400 55.32300 scale (grids/A): 2.895722 object centre (A): 14.38450 22.75000 3.241500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 290.6260 centred at (gu) : 94.01743 101.4981 91.06179 assigned negative charge : -285.6263 centred at (gu) : 94.31063 101.8888 90.87244 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 138439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17080 grid for indexing accessible points = 1.400000 m= 72373 mr = 100746 m= 27280 mr = 60596 m= 6085 mr = 22786 m= 731 mr = 4675 m= 63 mr = 460 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 5028 time to turn everything in is 1.040000 number of dielectric boundary points 55687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 14640 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) : 1.930481 object centre at (A) : 14.38450 22.75000 3.241500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.079518 7.8625180E-02 midg,1,midg; midg,igrid,midg 0.2348339 -1.7415052E-03 1,midg,midg; igrid,midg,midg 6.3340344E-02 1.0200784E-02 gauss-seidel spectral radius is 0.9992334 estimated iterations to convergence 285 setup time was (sec) 1.310000 now iterating at: 14:22:40 rms-change max change #iterations 8.624956 580.5063 at 10iterations 4.947174 138.7813 at 20iterations 2.817214 72.51328 at 30iterations 1.602332 36.89219 at 40iterations 0.9117777 17.44308 at 50iterations 0.5182008 11.34607 at 60iterations 0.2936126 6.717678 at 70iterations 0.1665111 3.362623 at 80iterations 9.4648883E-02 1.896954 at 90iterations 5.3710137E-02 1.062447 at 100iterations 3.0423854E-02 0.6034751 at 110iterations 1.7296854E-02 0.3463669 at 120iterations 9.8241875E-03 0.2037134 at 130iterations 5.5672517E-03 0.1228695 at 140iterations 3.1614427E-03 7.8020096E-02 at 150iterations 1.7955336E-03 3.4290314E-02 at 160iterations 1.0178823E-03 2.2584438E-02 at 170iterations 5.7886011E-04 1.0604858E-02 at 180iterations finished qdiffx linear iterations at : 14:23:09 total time elapsed so far: 10.52000 # loops : 180 mean,max change (kT/e) : 5.7886011E-04 1.0604858E-02 energy calculations done at 10.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.69000 DelPhi exited at 14:23:10 10.691u 0.161s 0:37.60 28.8% 0+0k 0+0io 0pf+0w