Sun Oct 9 00:06:31 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 Sun Oct 9 2011 at 00:06:31 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2407 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6402763 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): -26.98100 26.66900 ymin,ymax (A): 8.019000 51.32700 zmin,zma (A): -12.11000 43.49100 x,y,z range (A): 53.65000 43.30800 55.60100 scale (grids/A): 0.6402763 object centre (A): -0.1559992 29.67300 15.69050 number of atom coordinates read : 2407 total number of charged atoms : 2272 net assigned charge : 10.51403 assigned positive charge : 353.8213 centred at (gu) : 90.62440 90.40656 90.70757 assigned negative charge : -343.3080 centred at (gu) : 90.66482 90.33661 90.75740 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6802 nv = 96 ne = 84 npr = 47522 no. pairs analyzed = 47522 no. exposed pairs = 3235 no. arc points = 23171 no. surface atoms = 1076 nbur = 1331 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 402 mr = 3492 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.1900000 number of dielectric boundary points 3659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2338 ## 239 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8075 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7781804E-08 1.1822557E-08 midg,1,midg; midg,igrid,midg 7.5141342E-09 2.4699913E-08 1,midg,midg; igrid,midg,midg 1.7245892E-08 1.2758539E-08 gauss-seidel spectral radius is 0.9873562 estimated iterations to convergence 73 setup time was (sec) 0.4000000 now iterating at: 00:06:31 rms-change max change #iterations 0.1367480 22.27107 at 10iterations 1.3272809E-02 2.192586 at 20iterations 1.3160332E-03 0.1706085 at 30iterations 1.3212598E-04 1.8003464E-02 at 40iterations 1.3754360E-05 2.0885468E-03 at 50iterations finished qdiffx linear iterations at : 00:06:34 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 1.3754360E-05 2.0885468E-03 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 00:06:35 3.613u 0.195s 0:04.06 93.5% 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 Sun Oct 9 2011 at 00:06:35 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2407 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.920829 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): -26.98100 26.66900 ymin,ymax (A): 8.019000 51.32700 zmin,zma (A): -12.11000 43.49100 x,y,z range (A): 53.65000 43.30800 55.60100 scale (grids/A): 1.920829 object centre (A): -0.1559992 29.67300 15.69050 number of atom coordinates read : 2407 total number of charged atoms : 2272 net assigned charge : 10.51403 assigned positive charge : 353.8213 centred at (gu) : 91.87278 91.21953 92.12253 assigned negative charge : -343.3080 centred at (gu) : 91.99447 91.00972 92.27213 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73112 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23171 grid for indexing accessible points = 1.400000 m= 25605 mr = 48720 m= 4143 mr = 18137 m= 275 mr = 2461 m= 1 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2119 time to turn everything in is 0.3700000 number of dielectric boundary points 33719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 17877 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) : 0.6402763 object centre at (A) : -0.1559992 29.67300 15.69050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9682047E-02 3.0770835E-02 midg,1,midg; midg,igrid,midg -1.3654632E-03 2.3284143E-02 1,midg,midg; igrid,midg,midg 4.8640192E-02 4.3923497E-02 gauss-seidel spectral radius is 0.9986534 estimated iterations to convergence 216 setup time was (sec) 0.6100000 now iterating at: 00:06:35 rms-change max change #iterations 4.076093 166.5614 at 10iterations 1.910428 89.47995 at 20iterations 0.8982100 31.51633 at 30iterations 0.4204207 14.19669 at 40iterations 0.1978402 6.299819 at 50iterations 9.2802331E-02 2.928806 at 60iterations 4.3711677E-02 1.474091 at 70iterations 2.0489329E-02 0.6557922 at 80iterations 9.6498551E-03 0.3146391 at 90iterations 4.5352862E-03 0.1512306 at 100iterations 2.1317913E-03 6.9734573E-02 at 110iterations 1.0002771E-03 3.4042358E-02 at 120iterations finished qdiffx linear iterations at : 00:06:43 total time elapsed so far: 8.190000 # loops : 120 mean,max change (kT/e) : 1.0002771E-03 3.4042358E-02 energy calculations done at 8.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.330000 DelPhi exited at 00:06:43 8.330u 0.225s 0:08.81 97.0% 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 Sun Oct 9 2011 at 00:06:44 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2407 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.881243 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): -26.98100 26.66900 ymin,ymax (A): 8.019000 51.32700 zmin,zma (A): -12.11000 43.49100 x,y,z range (A): 53.65000 43.30800 55.60100 scale (grids/A): 2.881243 object centre (A): -0.1559992 29.67300 15.69050 number of atom coordinates read : 2407 total number of charged atoms : 2272 net assigned charge : 10.51403 assigned positive charge : 353.8213 centred at (gu) : 92.80910 91.82931 93.18376 assigned negative charge : -343.3080 centred at (gu) : 92.99168 91.51466 93.40824 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 168804 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23171 grid for indexing accessible points = 1.400000 m= 82702 mr = 118659 m= 29910 mr = 65759 m= 7357 mr = 23373 m= 1229 mr = 5353 m= 78 mr = 850 m= 0 mr = 21 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 7138 time to turn everything in is 0.9600000 number of dielectric boundary points 76065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 18170 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) : 1.920829 object centre at (A) : -0.1559992 29.67300 15.69050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9487811 0.3722282 midg,1,midg; midg,igrid,midg -3.9096814E-02 0.2284111 1,midg,midg; igrid,midg,midg 0.4948495 0.4167714 gauss-seidel spectral radius is 0.9992726 estimated iterations to convergence 293 setup time was (sec) 1.220000 now iterating at: 00:06:45 rms-change max change #iterations 9.654438 381.5289 at 10iterations 5.695089 144.3977 at 20iterations 3.340244 81.95274 at 30iterations 1.949672 40.71810 at 40iterations 1.136131 23.13908 at 50iterations 0.6586464 15.05746 at 60iterations 0.3837696 8.606587 at 70iterations 0.2217267 4.669325 at 80iterations 0.1285549 2.419359 at 90iterations 7.4416727E-02 1.459854 at 100iterations 4.3086730E-02 0.7872491 at 110iterations 2.4831148E-02 0.4796877 at 120iterations 1.4357437E-02 0.2921829 at 130iterations 8.2996581E-03 0.1508908 at 140iterations 4.7958302E-03 9.1448307E-02 at 150iterations 2.7635484E-03 5.4534912E-02 at 160iterations 1.5983650E-03 2.8746605E-02 at 170iterations 9.2233502E-04 1.7013550E-02 at 180iterations finished qdiffx linear iterations at : 00:06:57 total time elapsed so far: 13.48000 # loops : 180 mean,max change (kT/e) : 9.2233502E-04 1.7013550E-02 energy calculations done at 13.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.61000 DelPhi exited at 00:06:58 13.607u 0.241s 0:14.10 98.1% 0+0k 0+0io 0pf+0w