Re: Chains, LEaP and ambpdb

From: David A. Case <>
Date: Tue 17 Dec 2002 19:28:21 -0800

On Tue, Dec 17, 2002, Luis Gracia wrote:
> >
> >>I constructed a system with LEaP that has more than 10000 waters. When
> >>converting the files to pdb with the program ambpdb I get **** in the
> >>residue number from 10000 up.
> >
> sorry, I forgot to say that I am using amber 6.

You can fix this with a two-line change to ambpdb.f. Here is what is
in amber7:

          J_print = mod(J+ioffset,10000)
          if (arg1.eq.'-pdb') then
            WRITE(NF,60) K,atnam,LBRES(J),J_print,(C(JC+M),M=1,3)

Here "J" is the real residue number, but J_print is what gets written
to the file, so that it is never greater than 9999. You could put this
change into your version of the code, (or update to the more recent version).

..hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Tue Dec 17 2002 - 19:28:21 PST
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