Sun Oct 9 06:03:33 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 06:03:33 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1866 !!! WARNING: HIR 132 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6511322 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): 18.66600 69.67900 ymin,ymax (A): 15.45900 70.13300 zmin,zma (A): 47.07000 93.57000 x,y,z range (A): 51.01300 54.67400 46.50000 scale (grids/A): 0.6511322 object centre (A): 44.17250 42.79600 70.32000 number of atom coordinates read : 1866 total number of charged atoms : 1724 net assigned charge : -8.985989 assigned positive charge : 290.6799 centred at (gu) : 90.05569 87.69655 88.53215 assigned negative charge : -299.6660 centred at (gu) : 90.29276 87.56597 88.85469 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5446 nv = 96 ne = 84 npr = 36536 no. pairs analyzed = 36536 no. exposed pairs = 2513 no. arc points = 18109 no. surface atoms = 850 nbur = 1016 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 280 mr = 2748 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.1600000 number of dielectric boundary points 2957 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1706 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6186 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7402194E-08 -4.2685645E-08 midg,1,midg; midg,igrid,midg -5.5069570E-08 -1.7442433E-09 1,midg,midg; igrid,midg,midg 9.8234780E-09 -4.7698833E-08 gauss-seidel spectral radius is 0.9877192 estimated iterations to convergence 74 setup time was (sec) 0.3300000 now iterating at: 06:03:34 rms-change max change #iterations 0.1374404 20.73516 at 10iterations 1.3628464E-02 2.398227 at 20iterations 1.3915726E-03 0.2248497 at 30iterations 1.4356736E-04 2.6546478E-02 at 40iterations 1.4254601E-05 2.2435188E-03 at 50iterations finished qdiffx linear iterations at : 06:03:36 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.4254601E-05 2.2435188E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 06:03:37 3.324u 0.175s 0:03.75 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 Sun Oct 9 2011 at 06:03:37 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1866 !!! WARNING: HIR 132 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.953397 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): 18.66600 69.67900 ymin,ymax (A): 15.45900 70.13300 zmin,zma (A): 47.07000 93.57000 x,y,z range (A): 51.01300 54.67400 46.50000 scale (grids/A): 1.953397 object centre (A): 44.17250 42.79600 70.32000 number of atom coordinates read : 1866 total number of charged atoms : 1724 net assigned charge : -8.985989 assigned positive charge : 290.6799 centred at (gu) : 90.16707 83.08952 85.59641 assigned negative charge : -299.6660 centred at (gu) : 90.87847 82.69794 86.56403 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 57743 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18109 grid for indexing accessible points = 1.400000 m= 19861 mr = 37585 m= 3016 mr = 14192 m= 177 mr = 1788 m= 3 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 522 time to turn everything in is 0.2900000 number of dielectric boundary points 27178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 13624 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) : 0.6511322 object centre at (A) : 44.17250 42.79600 70.32000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0180721E-03 -4.2298753E-02 midg,1,midg; midg,igrid,midg -9.5249668E-02 -2.1817001E-02 1,midg,midg; igrid,midg,midg 2.7179455E-02 -5.3930461E-02 gauss-seidel spectral radius is 0.9986292 estimated iterations to convergence 214 setup time was (sec) 0.5000000 now iterating at: 06:03:38 rms-change max change #iterations 3.839811 176.3456 at 10iterations 1.788612 72.55416 at 20iterations 0.8359120 29.30407 at 30iterations 0.3897280 16.73291 at 40iterations 0.1820060 6.768941 at 50iterations 8.4658302E-02 3.029682 at 60iterations 3.9429434E-02 1.373528 at 70iterations 1.8436521E-02 0.6803913 at 80iterations 8.5820025E-03 0.2968121 at 90iterations 4.0194741E-03 0.1361313 at 100iterations 1.8656617E-03 7.0999146E-02 at 110iterations 8.6982729E-04 3.4118652E-02 at 120iterations finished qdiffx linear iterations at : 06:03:45 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 8.6982729E-04 3.4118652E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 06:03:45 7.602u 0.198s 0:08.11 96.0% 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 06:03:45 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1866 !!! WARNING: HIR 132 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.930095 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): 18.66600 69.67900 ymin,ymax (A): 15.45900 70.13300 zmin,zma (A): 47.07000 93.57000 x,y,z range (A): 51.01300 54.67400 46.50000 scale (grids/A): 2.930095 object centre (A): 44.17250 42.79600 70.32000 number of atom coordinates read : 1866 total number of charged atoms : 1724 net assigned charge : -8.985989 assigned positive charge : 290.6799 centred at (gu) : 90.25049 79.63432 83.39452 assigned negative charge : -299.6660 centred at (gu) : 91.31767 79.04697 84.84607 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 133389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18109 grid for indexing accessible points = 1.400000 m= 64159 mr = 91414 m= 22448 mr = 51396 m= 5298 mr = 17598 m= 768 mr = 3851 m= 37 mr = 486 m= 0 mr = 8 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1758 time to turn everything in is 0.7300000 number of dielectric boundary points 61346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 13792 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) : 1.953397 object centre at (A) : 44.17250 42.79600 70.32000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8413961E-02 -0.4455717 midg,1,midg; midg,igrid,midg -0.8563531 -0.1618617 1,midg,midg; igrid,midg,midg 0.1352124 -0.8917095 gauss-seidel spectral radius is 0.9992457 estimated iterations to convergence 287 setup time was (sec) 0.9500000 now iterating at: 06:03:46 rms-change max change #iterations 9.078378 595.7843 at 10iterations 5.271143 138.0580 at 20iterations 3.015754 71.62569 at 30iterations 1.730886 36.06176 at 40iterations 0.9904450 22.46865 at 50iterations 0.5665571 12.72640 at 60iterations 0.3241974 7.340891 at 70iterations 0.1852171 3.953871 at 80iterations 0.1060139 2.341265 at 90iterations 6.0362350E-02 1.245003 at 100iterations 3.4473147E-02 0.7604836 at 110iterations 1.9679099E-02 0.4612122 at 120iterations 1.1221570E-02 0.2312012 at 130iterations 6.4029782E-03 0.1411114 at 140iterations 3.6507321E-03 7.6141357E-02 at 150iterations 2.0831039E-03 4.8532248E-02 at 160iterations 1.1915590E-03 2.4147034E-02 at 170iterations 6.7868578E-04 1.4243841E-02 at 180iterations finished qdiffx linear iterations at : 06:03:57 total time elapsed so far: 11.97000 # loops : 180 mean,max change (kT/e) : 6.7868578E-04 1.4243841E-02 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.11000 DelPhi exited at 06:03:58 12.114u 0.215s 0:12.59 97.8% 0+0k 0+0io 0pf+0w