Mon Oct 10 23:52:23 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 Mon Oct 10 2011 at 23:52:23 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 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: 0.5883228 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): 10.06800 64.70900 ymin,ymax (A): -1.242000 59.26900 zmin,zma (A): 10.18300 53.97600 x,y,z range (A): 54.64100 60.51100 43.79300 scale (grids/A): 0.5883228 object centre (A): 37.38850 29.01350 32.07950 number of atom coordinates read : 2623 total number of charged atoms : 2475 net assigned charge : 8.812017 assigned positive charge : 396.1909 centred at (gu) : 88.77632 90.71921 89.56501 assigned negative charge : -387.3794 centred at (gu) : 88.77795 90.60254 89.69480 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5928 nv = 96 ne = 84 npr = 52988 no. pairs analyzed = 52988 no. exposed pairs = 3154 no. arc points = 21783 no. surface atoms = 1063 nbur = 1560 mkacc time = 8.9999996E-02 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 = 1.456000 m= 257 mr = 3271 m= 0 mr = 13 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 0.2000000 number of dielectric boundary points 2901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2226 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7458 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3397825E-09 -7.0391881E-10 midg,1,midg; midg,igrid,midg -3.6441719E-10 6.3916570E-09 1,midg,midg; igrid,midg,midg 3.3745440E-09 1.8906348E-09 gauss-seidel spectral radius is 0.9850501 estimated iterations to convergence 67 setup time was (sec) 0.4000000 now iterating at: 23:52:24 rms-change max change #iterations 0.1040207 16.48882 at 10iterations 9.4768982E-03 1.328442 at 20iterations 1.2192504E-03 0.2535439 at 30iterations 2.7166624E-04 6.3732147E-02 at 40iterations 6.7142675E-05 1.6345978E-02 at 50iterations finished qdiffx linear iterations at : 23:52:27 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 6.7142675E-05 1.6345978E-02 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 23:52:28 3.510u 0.177s 0:04.34 84.7% 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 Mon Oct 10 2011 at 23:52:28 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 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: 1.764968 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): 10.06800 64.70900 ymin,ymax (A): -1.242000 59.26900 zmin,zma (A): 10.18300 53.97600 x,y,z range (A): 54.64100 60.51100 43.79300 scale (grids/A): 1.764968 object centre (A): 37.38850 29.01350 32.07950 number of atom coordinates read : 2623 total number of charged atoms : 2475 net assigned charge : 8.812017 assigned positive charge : 396.1909 centred at (gu) : 86.32807 92.15720 88.69463 assigned negative charge : -387.3794 centred at (gu) : 86.33370 91.80748 89.08438 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21783 grid for indexing accessible points = 1.400000 m= 21671 mr = 45093 m= 2740 mr = 15798 m= 80 mr = 1602 m= 0 mr = 9 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1484 time to turn everything in is 0.3200000 number of dielectric boundary points 26812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 19234 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) : 0.5883228 object centre at (A) : 37.38850 29.01350 32.07950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6779164E-02 3.7971074E-03 midg,1,midg; midg,igrid,midg -1.2568397E-02 -1.2906365E-02 1,midg,midg; igrid,midg,midg 2.4425844E-03 1.3683673E-02 gauss-seidel spectral radius is 0.9984115 estimated iterations to convergence 199 setup time was (sec) 0.5400000 now iterating at: 23:52:29 rms-change max change #iterations 3.652765 157.2525 at 10iterations 1.612597 64.91214 at 20iterations 0.7077211 30.48109 at 30iterations 0.3137696 12.58161 at 40iterations 0.1388969 5.089355 at 50iterations 6.1680187E-02 2.074672 at 60iterations 2.7318647E-02 1.105068 at 70iterations 1.2232725E-02 0.4179363 at 80iterations 5.5689728E-03 0.1892529 at 90iterations 2.6226132E-03 0.1110535 at 100iterations 1.3009600E-03 5.7060242E-02 at 110iterations 6.9552241E-04 3.2203674E-02 at 120iterations finished qdiffx linear iterations at : 23:52:36 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 6.9552241E-04 3.2203674E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 23:52:36 7.921u 0.209s 0:08.54 95.0% 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 Mon Oct 10 2011 at 23:52:36 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 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: 2.647453 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): 10.06800 64.70900 ymin,ymax (A): -1.242000 59.26900 zmin,zma (A): 10.18300 53.97600 x,y,z range (A): 54.64100 60.51100 43.79300 scale (grids/A): 2.647453 object centre (A): 37.38850 29.01350 32.07950 number of atom coordinates read : 2623 total number of charged atoms : 2475 net assigned charge : 8.812017 assigned positive charge : 396.1909 centred at (gu) : 84.49193 93.23571 88.04169 assigned negative charge : -387.3794 centred at (gu) : 84.50047 92.71135 88.62649 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 150511 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21783 grid for indexing accessible points = 1.400000 m= 73067 mr = 109920 m= 23519 mr = 59477 m= 4620 mr = 18598 m= 414 mr = 3338 m= 17 mr = 234 m= 0 mr = 2 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 5394 time to turn everything in is 0.7900000 number of dielectric boundary points 60579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 19790 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) : 1.764968 object centre at (A) : 37.38850 29.01350 32.07950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3258584 5.9218794E-02 midg,1,midg; midg,igrid,midg -0.3594061 -0.5422071 1,midg,midg; igrid,midg,midg -1.9363582E-02 0.1118711 gauss-seidel spectral radius is 0.9991893 estimated iterations to convergence 277 setup time was (sec) 1.040000 now iterating at: 23:52:38 rms-change max change #iterations 8.845854 357.1902 at 10iterations 4.974164 118.2145 at 20iterations 2.796567 59.51947 at 30iterations 1.571034 35.85855 at 40iterations 0.8795775 17.10024 at 50iterations 0.4909759 10.23457 at 60iterations 0.2764243 5.904930 at 70iterations 0.1546972 3.165340 at 80iterations 8.6588793E-02 1.698582 at 90iterations 4.8410334E-02 1.045174 at 100iterations 2.7152942E-02 0.5276747 at 110iterations 1.5277269E-02 0.3106651 at 120iterations 8.6525809E-03 0.1777649 at 130iterations 4.9350155E-03 9.7953796E-02 at 140iterations 2.8595536E-03 6.4147949E-02 at 150iterations 1.7054370E-03 3.9463043E-02 at 160iterations 1.0668193E-03 2.6973724E-02 at 170iterations 7.0053717E-04 1.8127441E-02 at 180iterations finished qdiffx linear iterations at : 23:52:49 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 7.0053717E-04 1.8127441E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 23:52:49 12.595u 0.217s 0:13.11 97.6% 0+0k 0+0io 0pf+0w