You are trying to create a pdb using ambpdb? If this is the case,
then these atom number/residue number limits are hard-coded into
ambpdb in the source code. If you want to add another order of
magnitude to the available residue number and atom number, you'll have
to change the Formats in $AMBERHOME/src/etc/ambpdb.f and recompile it.
In my version of ambpdb.f, these format statements are located around
line 790. (I believe you'll want to change I5 into I6 for atom numbers
and I4 into I5 for residue numbers, though I'm not comfortable enough
with fortran format statements to know if these changes alone will be
enough to accomplish what you're trying to).
Good luck!
Jason
2010/1/7 Fernando Martín García <fmgarcia.cbm.uam.es>:
> Hello:
>
> I have problem with the identification number of residue and atom. The
> problem is that when residue is over 9999, the numeration change to
> ****. The problem is the same in atom number.
>
> I installed amber10 but i obtain the same result that in amber8. Can
> anybody help me to know if there is an option to modify the numeration?
>
> This is my result for residues
>
>
> ATOM 42297 H1 WAT 9998 137.785 -11.529 53.410 0.00 0.00
> ATOM 42298 H2 WAT 9998 137.132 -12.797 53.917 0.00 0.00
> ATOM 42299 O WAT 9999 103.772 58.806 9.424 0.00 0.00
> ATOM 42300 H1 WAT 9999 104.549 59.165 9.852 0.00 0.00
> ATOM 42301 H2 WAT 9999 103.107 58.786 10.113 0.00 0.00
> ATOM 42302 O WAT **** 82.586 -43.191 45.785 0.00 0.00
> ATOM 42303 H1 WAT **** 82.673 -42.371 46.270 0.00 0.00
> ATOM 42304 H2 WAT **** 82.388 -42.919 44.889 0.00 0.00
> ATOM 42305 O WAT **** 101.964 50.272 72.323 0.00 0.00
>
> and for atoms:
>
> ATOM 99996 H1 WAT **** 91.672 34.379 287.571 0.00 0.00
> ATOM 99997 H2 WAT **** 91.016 35.674 287.141 0.00 0.00
> ATOM 99998 O WAT **** -51.910 -10.370 11.200 0.00 0.00
> ATOM 99999 H1 WAT **** -51.086 -9.922 11.394 0.00 0.00
> ATOM ***** H2 WAT **** -52.292 -10.552 12.059 0.00 0.00
> ATOM ***** O WAT **** 16.143 -15.117 11.351 0.00 0.00
> ATOM ***** H1 WAT **** 15.335 -15.359 11.803 0.00 0.00
> ATOM ***** H2 WAT **** 16.467 -14.355 11.832 0.00 0.00
>
>
> Thank you
> --
> Fernando Martín García.
> Centro de Biología Molecular "Severo Ochoa".
> C/ Nicolás Cabrera, 1.
> Campus UAM. Cantoblanco, 28049 Madrid. Spain.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 07 2010 - 07:00:02 PST
