Sat Oct 15 13:37:55 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 Sat Oct 15 2011 at 13:37:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3495 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: 0.5563543 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): -29.69400 30.69000 ymin,ymax (A): -47.06900 6.543000 zmin,zma (A): 66.42200 130.4100 x,y,z range (A): 60.38400 53.61200 63.98801 scale (grids/A): 0.5563543 object centre (A): 0.4980001 -20.26300 98.41600 number of atom coordinates read : 3495 total number of charged atoms : 3341 net assigned charge : 14.00003 assigned positive charge : 520.8007 centred at (gu) : 91.00337 90.55143 91.87689 assigned negative charge : -506.8021 centred at (gu) : 90.97589 90.51844 91.90517 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7505 nv = 96 ne = 84 npr = 63239 no. pairs analyzed = 63239 no. exposed pairs = 5624 no. arc points = 40295 no. surface atoms = 1843 nbur = 1652 mkacc time = 0.1900000 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= 387 mr = 3214 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 4658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3935 ## 459 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 9483 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0304663E-09 1.5214991E-09 midg,1,midg; midg,igrid,midg 8.1668478E-10 1.8879303E-09 1,midg,midg; igrid,midg,midg 7.8412843E-10 2.0274225E-09 gauss-seidel spectral radius is 0.9834065 estimated iterations to convergence 64 setup time was (sec) 0.7100000 now iterating at: 13:37:57 rms-change max change #iterations 8.4038839E-02 13.71076 at 10iterations 5.9252726E-03 0.8896465 at 20iterations 5.7306403E-04 0.1035538 at 30iterations 1.2326745E-04 1.2054443E-02 at 40iterations 3.5355130E-05 3.0665398E-03 at 50iterations finished qdiffx linear iterations at : 13:38:04 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 3.5355130E-05 3.0665398E-03 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 13:38:05 4.320u 0.291s 0:09.40 49.0% 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 Sat Oct 15 2011 at 13:38:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3495 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: 1.669063 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): -29.69400 30.69000 ymin,ymax (A): -47.06900 6.543000 zmin,zma (A): 66.42200 130.4100 x,y,z range (A): 60.38400 53.61200 63.98801 scale (grids/A): 1.669063 object centre (A): 0.4980001 -20.26300 98.41600 number of atom coordinates read : 3495 total number of charged atoms : 3341 net assigned charge : 14.00003 assigned positive charge : 520.8007 centred at (gu) : 93.00929 91.65367 95.62991 assigned negative charge : -506.8021 centred at (gu) : 92.92699 91.55494 95.71530 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 80566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40295 grid for indexing accessible points = 1.400000 m= 26625 mr = 49106 m= 3450 mr = 16983 m= 115 mr = 1474 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 43189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 392 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 25690 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) : 0.5563543 object centre at (A) : 0.4980001 -20.26300 98.41600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6087044E-02 5.0382074E-03 midg,1,midg; midg,igrid,midg 9.7071361E-03 2.8897496E-02 1,midg,midg; igrid,midg,midg -3.6609292E-02 1.8400989E-02 gauss-seidel spectral radius is 0.9983665 estimated iterations to convergence 196 setup time was (sec) 1.090000 now iterating at: 13:38:09 rms-change max change #iterations 3.766414 154.8286 at 10iterations 1.631422 60.99614 at 20iterations 0.7093391 23.33949 at 30iterations 0.3069755 10.63004 at 40iterations 0.1335046 4.288657 at 50iterations 5.8096629E-02 2.012146 at 60iterations 2.5304643E-02 0.8788931 at 70iterations 1.1036523E-02 0.3986330 at 80iterations 4.8209839E-03 0.1645746 at 90iterations 2.1077702E-03 7.7044487E-02 at 100iterations 9.2449278E-04 2.9973030E-02 at 110iterations 4.1213445E-04 1.4143944E-02 at 120iterations finished qdiffx linear iterations at : 13:38:32 total time elapsed so far: 9.860000 # loops : 120 mean,max change (kT/e) : 4.1213445E-04 1.4143944E-02 energy calculations done at 9.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.04000 DelPhi exited at 13:38:33 10.043u 0.330s 0:28.34 36.5% 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 Sat Oct 15 2011 at 13:38:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3495 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: 2.503594 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): -29.69400 30.69000 ymin,ymax (A): -47.06900 6.543000 zmin,zma (A): 66.42200 130.4100 x,y,z range (A): 60.38400 53.61200 63.98801 scale (grids/A): 2.503594 object centre (A): 0.4980001 -20.26300 98.41600 number of atom coordinates read : 3495 total number of charged atoms : 3341 net assigned charge : 14.00003 assigned positive charge : 520.8007 centred at (gu) : 94.51368 92.48003 98.44462 assigned negative charge : -506.8021 centred at (gu) : 94.39051 92.33241 98.57291 start vw surface at 0.1700000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 185615 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40295 grid for indexing accessible points = 1.400000 m= 87515 mr = 121313 m= 28684 mr = 65162 m= 5292 mr = 20317 m= 383 mr = 3130 m= 8 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.880000 number of dielectric boundary points 97444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 26708 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) : 1.669063 object centre at (A) : 0.4980001 -20.26300 98.41600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2147389 0.1066288 midg,1,midg; midg,igrid,midg 2.2904648E-02 0.3718407 1,midg,midg; igrid,midg,midg -0.8332919 0.3082304 gauss-seidel spectral radius is 0.9992397 estimated iterations to convergence 286 setup time was (sec) 2.220000 now iterating at: 13:38:39 rms-change max change #iterations 10.18673 374.4832 at 10iterations 6.126529 169.7364 at 20iterations 3.638601 104.6858 at 30iterations 2.143508 48.99709 at 40iterations 1.254865 26.75444 at 50iterations 0.7300422 16.06753 at 60iterations 0.4227070 9.207367 at 70iterations 0.2439833 4.910382 at 80iterations 0.1407736 2.884135 at 90iterations 8.0859430E-02 1.611486 at 100iterations 4.6388537E-02 1.051002 at 110iterations 2.6607387E-02 0.5137830 at 120iterations 1.5230143E-02 0.2930219 at 130iterations 8.7010004E-03 0.1733112 at 140iterations 4.9751066E-03 0.1034355 at 150iterations 2.8468326E-03 5.5049896E-02 at 160iterations 1.6284370E-03 3.3323288E-02 at 170iterations 9.2886441E-04 1.7591715E-02 at 180iterations finished qdiffx linear iterations at : 13:39:15 total time elapsed so far: 17.21000 # loops : 180 mean,max change (kT/e) : 9.2886441E-04 1.7591715E-02 energy calculations done at 17.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.39000 DelPhi exited at 13:39:16 17.389u 0.388s 0:43.29 41.0% 0+0k 0+0io 0pf+0w