Tue Oct 11 05:28:23 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 Tue Oct 11 2011 at 05:28:23 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.6994793 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): 25.62200 72.86100 ymin,ymax (A): -20.99200 29.90300 zmin,zma (A): 3.844000 46.52400 x,y,z range (A): 47.23900 50.89500 42.68000 scale (grids/A): 0.6994793 object centre (A): 49.24150 4.455501 25.18400 number of atom coordinates read : 2053 total number of charged atoms : 1923 net assigned charge : 6.039010 assigned positive charge : 313.5410 centred at (gu) : 88.71529 91.16144 90.13390 assigned negative charge : -307.5021 centred at (gu) : 88.82973 91.07520 90.20660 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6862 nv = 96 ne = 84 npr = 41006 no. pairs analyzed = 41006 no. exposed pairs = 2524 no. arc points = 17186 no. surface atoms = 857 nbur = 1196 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 406 mr = 3885 m= 2 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1628 ## 156 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 7644 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8494657E-08 1.1461931E-08 midg,1,midg; midg,igrid,midg 4.9244648E-09 9.5130673E-08 1,midg,midg; igrid,midg,midg 1.1205780E-07 -4.1848760E-09 gauss-seidel spectral radius is 0.9893462 estimated iterations to convergence 79 setup time was (sec) 0.5000000 now iterating at: 05:28:23 rms-change max change #iterations 0.1910659 29.01191 at 10iterations 2.3471383E-02 3.635681 at 20iterations 3.2159807E-03 0.4165459 at 30iterations 6.0506945E-04 8.9702606E-02 at 40iterations 1.6390614E-04 2.0149231E-02 at 50iterations finished qdiffx linear iterations at : 05:28:27 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 1.6390614E-04 2.0149231E-02 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.390000 DelPhi exited at 05:28:28 4.390u 0.381s 0:05.06 94.2% 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 05:28:28 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.098438 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): 25.62200 72.86100 ymin,ymax (A): -20.99200 29.90300 zmin,zma (A): 3.844000 46.52400 x,y,z range (A): 47.23900 50.89500 42.68000 scale (grids/A): 2.098438 object centre (A): 49.24150 4.455501 25.18400 number of atom coordinates read : 2053 total number of charged atoms : 1923 net assigned charge : 6.039010 assigned positive charge : 313.5410 centred at (gu) : 86.14592 93.48461 90.40179 assigned negative charge : -307.5021 centred at (gu) : 86.48944 93.22568 90.62000 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17186 grid for indexing accessible points = 1.400000 m= 29219 mr = 51174 m= 5600 mr = 22342 m= 444 mr = 3687 m= 9 mr = 217 m= 0 mr = 3 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 30233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15254 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) : 0.6994793 object centre at (A) : 49.24150 4.455501 25.18400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3992967E-02 2.3489013E-02 midg,1,midg; midg,igrid,midg 3.0514300E-02 4.3823030E-02 1,midg,midg; igrid,midg,midg 4.1654337E-02 -3.4050718E-02 gauss-seidel spectral radius is 0.9988054 estimated iterations to convergence 229 setup time was (sec) 0.9300000 now iterating at: 05:28:29 rms-change max change #iterations 4.498094 203.5888 at 10iterations 2.202349 71.65591 at 20iterations 1.085852 34.43811 at 30iterations 0.5356527 16.92036 at 40iterations 0.2644615 7.891810 at 50iterations 0.1300562 3.981373 at 60iterations 6.3839927E-02 1.927773 at 70iterations 3.1775925E-02 0.9884186 at 80iterations 1.5849376E-02 0.5086555 at 90iterations 7.9583246E-03 0.2351799 at 100iterations 4.0441607E-03 0.1229162 at 110iterations 2.1309140E-03 6.9862366E-02 at 120iterations finished qdiffx linear iterations at : 05:28:38 total time elapsed so far: 10.36000 # loops : 120 mean,max change (kT/e) : 2.1309140E-03 6.9862366E-02 energy calculations done at 10.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.53000 DelPhi exited at 05:28:39 10.532u 0.432s 0:11.46 95.6% 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 05:28:39 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.147657 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): 25.62200 72.86100 ymin,ymax (A): -20.99200 29.90300 zmin,zma (A): 3.844000 46.52400 x,y,z range (A): 47.23900 50.89500 42.68000 scale (grids/A): 3.147657 object centre (A): 49.24150 4.455501 25.18400 number of atom coordinates read : 2053 total number of charged atoms : 1923 net assigned charge : 6.039010 assigned positive charge : 313.5410 centred at (gu) : 84.21880 95.22691 90.60268 assigned negative charge : -307.5021 centred at (gu) : 84.73415 94.83855 90.92999 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 166613 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17186 grid for indexing accessible points = 1.400000 m= 90934 mr = 123233 m= 37200 mr = 75703 m= 10455 mr = 30611 m= 2002 mr = 8207 m= 193 mr = 1426 m= 10 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.890000 number of dielectric boundary points 68108 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 15384 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) : 2.098438 object centre at (A) : 49.24150 4.455501 25.18400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1554818 0.2000178 midg,1,midg; midg,igrid,midg 0.2211254 0.3534596 1,midg,midg; igrid,midg,midg 0.3776577 -0.3561391 gauss-seidel spectral radius is 0.9992896 estimated iterations to convergence 296 setup time was (sec) 2.230000 now iterating at: 05:28:42 rms-change max change #iterations 10.06362 491.9395 at 10iterations 5.929307 139.5825 at 20iterations 3.492307 81.20480 at 30iterations 2.052850 39.41122 at 40iterations 1.202238 24.75108 at 50iterations 0.7057348 13.65036 at 60iterations 0.4136615 7.944765 at 70iterations 0.2423608 4.199348 at 80iterations 0.1415031 2.650151 at 90iterations 8.2828753E-02 1.526281 at 100iterations 4.8637722E-02 0.8987455 at 110iterations 2.8707324E-02 0.5987167 at 120iterations 1.7132068E-02 0.3110600 at 130iterations 1.0420238E-02 0.2035751 at 140iterations 6.5593901E-03 0.1298714 at 150iterations 4.3252306E-03 8.5834503E-02 at 160iterations 3.0332394E-03 5.9700012E-02 at 170iterations 2.2498246E-03 4.2301178E-02 at 180iterations finished qdiffx linear iterations at : 05:28:58 total time elapsed so far: 18.27000 # loops : 180 mean,max change (kT/e) : 2.2498246E-03 4.2301178E-02 energy calculations done at 18.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.44000 DelPhi exited at 05:28:58 18.443u 0.456s 0:19.23 98.2% 0+0k 0+0io 0pf+0w