Tue Oct 11 08:22:06 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 08:22:07 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6065252 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): -12.84600 36.95200 ymin,ymax (A): -26.94800 21.48100 zmin,zma (A): -13.28900 45.40600 x,y,z range (A): 49.79800 48.42900 58.69500 scale (grids/A): 0.6065252 object centre (A): 12.05300 -2.733500 16.05850 number of atom coordinates read : 2826 total number of charged atoms : 2671 net assigned charge : -0.8599864 assigned positive charge : 427.4656 centred at (gu) : 90.45933 90.55079 92.45590 assigned negative charge : -428.3262 centred at (gu) : 90.18957 90.43448 92.33301 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6757 nv = 96 ne = 84 npr = 58331 no. pairs analyzed = 58331 no. exposed pairs = 3322 no. arc points = 23342 no. surface atoms = 1119 nbur = 1707 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 306 mr = 3791 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3400000 number of dielectric boundary points 3256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2383 ## 263 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8471 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9039976E-09 9.2783496E-09 midg,1,midg; midg,igrid,midg -5.6933533E-09 5.5830283E-09 1,midg,midg; igrid,midg,midg -1.2869825E-08 1.3438717E-08 gauss-seidel spectral radius is 0.9859407 estimated iterations to convergence 69 setup time was (sec) 0.5600000 now iterating at: 08:22:07 rms-change max change #iterations 0.1206748 24.30312 at 10iterations 1.0834226E-02 1.589071 at 20iterations 1.0468967E-03 0.1418533 at 30iterations 1.4303683E-04 2.2113800E-02 at 40iterations 3.3371256E-05 4.3334961E-03 at 50iterations finished qdiffx linear iterations at : 08:22:10 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 3.3371256E-05 4.3334961E-03 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 08:22:10 3.187u 0.136s 0:03.81 86.8% 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 08:22:10 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.819576 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): -12.84600 36.95200 ymin,ymax (A): -26.94800 21.48100 zmin,zma (A): -13.28900 45.40600 x,y,z range (A): 49.79800 48.42900 58.69500 scale (grids/A): 1.819576 object centre (A): 12.05300 -2.733500 16.05850 number of atom coordinates read : 2826 total number of charged atoms : 2671 net assigned charge : -0.8599864 assigned positive charge : 427.4656 centred at (gu) : 91.37731 91.65181 97.36710 assigned negative charge : -428.3262 centred at (gu) : 90.56855 91.30317 96.99877 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 73654 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23342 grid for indexing accessible points = 1.400000 m= 25897 mr = 51847 m= 3384 mr = 19289 m= 121 mr = 1957 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 936 time to turn everything in is 0.5400000 number of dielectric boundary points 29939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 206 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 20881 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) : 0.6065252 object centre at (A) : 12.05300 -2.733500 16.05850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7007206E-02 1.3669474E-04 midg,1,midg; midg,igrid,midg -9.3697086E-03 1.3028115E-02 1,midg,midg; igrid,midg,midg -8.1286225E-03 3.6723353E-02 gauss-seidel spectral radius is 0.9985234 estimated iterations to convergence 206 setup time was (sec) 0.8200000 now iterating at: 08:22:11 rms-change max change #iterations 4.091219 218.8217 at 10iterations 1.858673 70.42419 at 20iterations 0.8459921 26.87138 at 30iterations 0.3837159 14.55188 at 40iterations 0.1754753 5.505890 at 50iterations 7.9806224E-02 3.253418 at 60iterations 3.6428977E-02 1.077332 at 70iterations 1.6584916E-02 0.5855694 at 80iterations 7.5980104E-03 0.2424436 at 90iterations 3.4895837E-03 0.1287451 at 100iterations 1.6236448E-03 5.0697327E-02 at 110iterations 7.6389429E-04 2.8878689E-02 at 120iterations finished qdiffx linear iterations at : 08:22:17 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 7.6389429E-04 2.8878689E-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 08:22:18 7.086u 0.196s 0:07.81 93.0% 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 Oct 11 2011 at 08:22:18 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.729363 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): -12.84600 36.95200 ymin,ymax (A): -26.94800 21.48100 zmin,zma (A): -13.28900 45.40600 x,y,z range (A): 49.79800 48.42900 58.69500 scale (grids/A): 2.729363 object centre (A): 12.05300 -2.733500 16.05850 number of atom coordinates read : 2826 total number of charged atoms : 2671 net assigned charge : -0.8599864 assigned positive charge : 427.4656 centred at (gu) : 92.06590 92.47755 101.0505 assigned negative charge : -428.3262 centred at (gu) : 90.85267 91.95473 100.4980 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 170739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23342 grid for indexing accessible points = 1.400000 m= 85999 mr = 125782 m= 28536 mr = 70860 m= 5672 mr = 22785 m= 593 mr = 4155 m= 22 mr = 348 m= 0 mr = 2 time to grow re-entrant surface = 0.7599999 no. cavity mid-points inaccessible to solvent = 3079 time to turn everything in is 1.320000 number of dielectric boundary points 67629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 21362 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) : 1.819576 object centre at (A) : 12.05300 -2.733500 16.05850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.360053 0.1120385 midg,1,midg; midg,igrid,midg -0.1150844 0.1705968 1,midg,midg; igrid,midg,midg -6.9086991E-02 0.3406884 gauss-seidel spectral radius is 0.9992268 estimated iterations to convergence 284 setup time was (sec) 1.610000 now iterating at: 08:22:20 rms-change max change #iterations 9.708344 289.8366 at 10iterations 5.588613 136.2100 at 20iterations 3.203948 67.59509 at 30iterations 1.834446 36.08643 at 40iterations 1.044275 21.27111 at 50iterations 0.5969569 11.63579 at 60iterations 0.3402177 6.190792 at 70iterations 0.1939977 3.998377 at 80iterations 0.1103522 2.215751 at 90iterations 6.2839910E-02 1.131311 at 100iterations 3.5746738E-02 0.6384621 at 110iterations 2.0354947E-02 0.3789444 at 120iterations 1.1590636E-02 0.2097740 at 130iterations 6.6320575E-03 0.1167755 at 140iterations 3.8036800E-03 8.4243774E-02 at 150iterations 2.2002270E-03 3.8925171E-02 at 160iterations 1.2846347E-03 2.4795532E-02 at 170iterations 7.6095050E-04 1.5876770E-02 at 180iterations finished qdiffx linear iterations at : 08:22:30 total time elapsed so far: 11.71000 # loops : 180 mean,max change (kT/e) : 7.6095050E-04 1.5876770E-02 energy calculations done at 11.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.89000 DelPhi exited at 08:22:31 11.890u 0.196s 0:12.52 96.4% 0+0k 0+0io 0pf+0w