Tue Oct 11 06:49:47 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 06:49:48 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2942 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5573735 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): -20.75700 43.11400 ymin,ymax (A): 21.92600 78.75300 zmin,zma (A): -71.24700 -22.49100 x,y,z range (A): 63.87100 56.82700 48.75600 scale (grids/A): 0.5573735 object centre (A): 11.17850 50.33950 -46.86900 number of atom coordinates read : 2942 total number of charged atoms : 2803 net assigned charge : -0.4859959 assigned positive charge : 429.7917 centred at (gu) : 90.09993 89.87567 89.27110 assigned negative charge : -430.2783 centred at (gu) : 90.09844 89.96434 89.26533 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6094 nv = 96 ne = 84 npr = 59885 no. pairs analyzed = 59885 no. exposed pairs = 3685 no. arc points = 26096 no. surface atoms = 1256 nbur = 1686 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 263 mr = 3231 m= 0 mr = 17 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2615 ## 297 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2367563E-10 7.2351465E-12 midg,1,midg; midg,igrid,midg 8.3469859E-10 -8.9495839E-10 1,midg,midg; igrid,midg,midg -6.0319631E-11 -3.3472256E-11 gauss-seidel spectral radius is 0.9833987 estimated iterations to convergence 64 setup time was (sec) 0.6800000 now iterating at: 06:49:48 rms-change max change #iterations 8.1771880E-02 14.54845 at 10iterations 5.8324030E-03 0.9907455 at 20iterations 4.1364896E-04 6.1574936E-02 at 30iterations 2.9929430E-05 5.4054260E-03 at 40iterations 2.5384679E-06 4.4822693E-04 at 50iterations finished qdiffx linear iterations at : 06:49:52 total time elapsed so far: 4.430000 # loops : 50 mean,max change (kT/e) : 2.5384679E-06 4.4822693E-04 energy calculations done at 4.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.600000 DelPhi exited at 06:49:53 4.600u 0.268s 0:05.80 83.7% 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 06:49:54 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2942 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.672120 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): -20.75700 43.11400 ymin,ymax (A): 21.92600 78.75300 zmin,zma (A): -71.24700 -22.49100 x,y,z range (A): 63.87100 56.82700 48.75600 scale (grids/A): 1.672120 object centre (A): 11.17850 50.33950 -46.86900 number of atom coordinates read : 2942 total number of charged atoms : 2803 net assigned charge : -0.4859959 assigned positive charge : 429.7917 centred at (gu) : 90.29930 89.62643 87.81302 assigned negative charge : -430.2783 centred at (gu) : 90.29496 89.89269 87.79550 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 66568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26096 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 22264 mr = 45372 m= 2500 mr = 15886 m= 61 mr = 1351 m= 0 mr = 6 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 28778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 277 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21626 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) : 0.5573735 object centre at (A) : 11.17850 50.33950 -46.86900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4034724E-03 1.0519869E-02 midg,1,midg; midg,igrid,midg -3.5863831E-03 5.0123790E-03 1,midg,midg; igrid,midg,midg 4.5911586E-03 -8.1665069E-03 gauss-seidel spectral radius is 0.9982768 estimated iterations to convergence 191 setup time was (sec) 0.8600000 now iterating at: 06:49:55 rms-change max change #iterations 3.453431 187.1726 at 10iterations 1.467134 71.16286 at 20iterations 0.6268386 22.89041 at 30iterations 0.2673426 9.169301 at 40iterations 0.1145404 4.334360 at 50iterations 4.8730277E-02 1.704615 at 60iterations 2.0741355E-02 0.7564354 at 70iterations 8.8908002E-03 0.3149109 at 80iterations 3.7779529E-03 0.1373892 at 90iterations 1.6171514E-03 6.1996460E-02 at 100iterations 6.8918773E-04 2.4958611E-02 at 110iterations 2.9576893E-04 1.0735035E-02 at 120iterations finished qdiffx linear iterations at : 06:50:04 total time elapsed so far: 10.61000 # loops : 120 mean,max change (kT/e) : 2.9576893E-04 1.0735035E-02 energy calculations done at 10.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.79000 DelPhi exited at 06:50:05 10.792u 0.281s 0:11.89 93.1% 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 06:50:06 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2942 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.508180 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): -20.75700 43.11400 ymin,ymax (A): 21.92600 78.75300 zmin,zma (A): -71.24700 -22.49100 x,y,z range (A): 63.87100 56.82700 48.75600 scale (grids/A): 2.508180 object centre (A): 11.17850 50.33950 -46.86900 number of atom coordinates read : 2942 total number of charged atoms : 2803 net assigned charge : -0.4859959 assigned positive charge : 429.7917 centred at (gu) : 90.44891 89.43951 86.71925 assigned negative charge : -430.2783 centred at (gu) : 90.44241 89.83908 86.69324 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 154303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26096 grid for indexing accessible points = 1.400000 m= 74569 mr = 110531 m= 23551 mr = 60018 m= 4155 mr = 18288 m= 292 mr = 2893 m= 2 mr = 156 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 64986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 22407 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) : 1.672120 object centre at (A) : 11.17850 50.33950 -46.86900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4814353E-02 0.1739734 midg,1,midg; midg,igrid,midg -5.0351575E-02 7.2992429E-02 1,midg,midg; igrid,midg,midg -1.4231500E-02 -0.1418685 gauss-seidel spectral radius is 0.9991680 estimated iterations to convergence 274 setup time was (sec) 1.370000 now iterating at: 06:50:07 rms-change max change #iterations 8.750679 368.2904 at 10iterations 4.952709 144.6664 at 20iterations 2.789169 57.86095 at 30iterations 1.565953 32.50372 at 40iterations 0.8789093 18.06744 at 50iterations 0.4894456 10.87651 at 60iterations 0.2734203 6.112988 at 70iterations 0.1522373 3.097365 at 80iterations 8.4794633E-02 1.621822 at 90iterations 4.6991486E-02 1.021688 at 100iterations 2.6213549E-02 0.5044467 at 110iterations 1.4561139E-02 0.2805481 at 120iterations 8.0760568E-03 0.1557703 at 130iterations 4.4939420E-03 9.6340179E-02 at 140iterations 2.4863342E-03 5.1918030E-02 at 150iterations 1.3874192E-03 2.8265357E-02 at 160iterations 7.6820049E-04 1.5964642E-02 at 170iterations 4.2571101E-04 7.9965591E-03 at 180iterations finished qdiffx linear iterations at : 06:50:17 total time elapsed so far: 10.93000 # loops : 180 mean,max change (kT/e) : 4.2571101E-04 7.9965591E-03 energy calculations done at 10.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.09000 DelPhi exited at 06:50:17 11.091u 0.246s 0:11.66 97.1% 0+0k 0+0io 0pf+0w