Mon Oct 10 18:31:00 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 18:31:00 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 !!! WARNING: HIR 257 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: 0.7057610 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): -41.27900 3.752000 ymin,ymax (A): 56.40100 106.8430 zmin,zma (A): -20.52900 29.41200 x,y,z range (A): 45.03100 50.44201 49.94100 scale (grids/A): 0.7057610 object centre (A): -18.76350 81.62200 4.441500 number of atom coordinates read : 2392 total number of charged atoms : 2255 net assigned charge : 1.014006 assigned positive charge : 359.7379 centred at (gu) : 89.08047 87.14594 88.70930 assigned negative charge : -358.7245 centred at (gu) : 88.98978 87.25595 88.67767 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7816 nv = 96 ne = 84 npr = 50337 no. pairs analyzed = 50337 no. exposed pairs = 2838 no. arc points = 19384 no. surface atoms = 971 nbur = 1421 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 473 mr = 4479 m= 6 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 69 time to turn everything in is 0.1800000 number of dielectric boundary points 3753 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1738 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9013 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3337041E-08 1.8764784E-08 midg,1,midg; midg,igrid,midg 1.1746292E-07 -3.0188396E-08 1,midg,midg; igrid,midg,midg -5.1283635E-08 4.6473854E-08 gauss-seidel spectral radius is 0.9895634 estimated iterations to convergence 80 setup time was (sec) 0.3800000 now iterating at: 18:31:01 rms-change max change #iterations 0.2157100 31.12361 at 10iterations 2.6367713E-02 3.838799 at 20iterations 3.2654305E-03 0.4457188 at 30iterations 4.1169752E-04 6.2593937E-02 at 40iterations 5.7465761E-05 8.0718994E-03 at 50iterations finished qdiffx linear iterations at : 18:31:03 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 5.7465761E-05 8.0718994E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 18:31:04 3.400u 0.167s 0:03.95 90.1% 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 18:31:04 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 !!! WARNING: HIR 257 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.117283 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): -41.27900 3.752000 ymin,ymax (A): 56.40100 106.8430 zmin,zma (A): -20.52900 29.41200 x,y,z range (A): 45.03100 50.44201 49.94100 scale (grids/A): 2.117283 object centre (A): -18.76350 81.62200 4.441500 number of atom coordinates read : 2392 total number of charged atoms : 2255 net assigned charge : 1.014006 assigned positive charge : 359.7379 centred at (gu) : 87.24093 81.43725 86.12748 assigned negative charge : -358.7245 centred at (gu) : 86.96927 81.76743 86.03265 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82724 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19384 grid for indexing accessible points = 1.400000 m= 32214 mr = 58282 m= 6144 mr = 24504 m= 511 mr = 4074 m= 10 mr = 227 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1619 time to turn everything in is 0.4200000 number of dielectric boundary points 34514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17927 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) : 0.7057610 object centre at (A) : -18.76350 81.62200 4.441500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1565744E-02 2.9476400E-02 midg,1,midg; midg,igrid,midg 4.4944055E-02 -4.5102858E-03 1,midg,midg; igrid,midg,midg 4.1689017E-04 1.9672904E-02 gauss-seidel spectral radius is 0.9988475 estimated iterations to convergence 233 setup time was (sec) 0.6400000 now iterating at: 18:31:05 rms-change max change #iterations 5.003816 183.7999 at 10iterations 2.470654 82.09626 at 20iterations 1.230915 34.40965 at 30iterations 0.6173847 18.95686 at 40iterations 0.3065070 9.520144 at 50iterations 0.1532708 4.477882 at 60iterations 7.6283216E-02 2.032021 at 70iterations 3.8014542E-02 1.051838 at 80iterations 1.8943351E-02 0.5551796 at 90iterations 9.4383163E-03 0.2816696 at 100iterations 4.7000702E-03 0.1353645 at 110iterations 2.3554564E-03 6.4018250E-02 at 120iterations finished qdiffx linear iterations at : 18:31:12 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 2.3554564E-03 6.4018250E-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) 7.880000 DelPhi exited at 18:31:12 7.886u 0.233s 0:08.46 95.8% 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 Mon Oct 10 2011 at 18:31:13 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 !!! WARNING: HIR 257 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: 3.175925 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): -41.27900 3.752000 ymin,ymax (A): 56.40100 106.8430 zmin,zma (A): -20.52900 29.41200 x,y,z range (A): 45.03100 50.44201 49.94100 scale (grids/A): 3.175925 object centre (A): -18.76350 81.62200 4.441500 number of atom coordinates read : 2392 total number of charged atoms : 2255 net assigned charge : 1.014006 assigned positive charge : 359.7379 centred at (gu) : 85.86124 77.15579 84.19105 assigned negative charge : -358.7245 centred at (gu) : 85.45375 77.65104 84.04894 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 191041 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19384 grid for indexing accessible points = 1.400000 m= 100068 mr = 140665 m= 40827 mr = 83333 m= 11417 mr = 33562 m= 2026 mr = 8813 m= 215 mr = 1425 m= 10 mr = 136 m= 0 mr = 3 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 5465 time to turn everything in is 1.290000 number of dielectric boundary points 77667 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 18040 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) : 2.117283 object centre at (A) : -18.76350 81.62200 4.441500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1706788 0.8422074 midg,1,midg; midg,igrid,midg 0.3487472 -3.2458551E-02 1,midg,midg; igrid,midg,midg 5.3776894E-02 6.5597638E-02 gauss-seidel spectral radius is 0.9993069 estimated iterations to convergence 300 setup time was (sec) 1.540000 now iterating at: 18:31:14 rms-change max change #iterations 11.14571 356.8692 at 10iterations 6.585101 117.5437 at 20iterations 3.884832 68.42300 at 30iterations 2.282080 38.80531 at 40iterations 1.346148 23.72761 at 50iterations 0.7905043 13.27590 at 60iterations 0.4629629 8.017044 at 70iterations 0.2714157 4.440346 at 80iterations 0.1591588 2.695789 at 90iterations 9.3151249E-02 1.568696 at 100iterations 5.4564390E-02 0.8774862 at 110iterations 3.1967465E-02 0.5274277 at 120iterations 1.8678883E-02 0.2965145 at 130iterations 1.0951093E-02 0.1757734 at 140iterations 6.4033978E-03 0.1085534 at 150iterations 3.7513096E-03 6.4025879E-02 at 160iterations 2.1937788E-03 3.4835815E-02 at 170iterations 1.2846889E-03 2.1030426E-02 at 180iterations finished qdiffx linear iterations at : 18:31:26 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 1.2846889E-03 2.1030426E-02 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 18:31:26 13.161u 0.233s 0:13.83 96.8% 0+0k 0+0io 0pf+0w