AMBER Archive (2005)

Subject: Re: AMBER: ambpdb TER problems

From: David A. Case (case_at_scripps.edu)
Date: Fri Dec 23 2005 - 19:53:50 CST

On Fri, Dec 23, 2005, Sam wrote:
>
> and found several problems in the newly created pdb file:
> (1) The terminal protein residue (CSER) is incorrectly
> identified as nonterminal ("SER").

This is not incorrect: the pdb format does not use special resdiue names
for beginning or terminal residues. Hence, "SER" is correct.

> (2) No TER card is inserted
> between this residue (SER) and the starting terminal residue
> (DA5) of the first DNA strand. (3) A TER card is incorrectly
> inserted partway into the DA5 residue.

This is weird, and I have not seen this behavior before. I suspect you will
have to post your prmtop file, or the procedure you used to create it.
Are you sure that the names and numbers of the input pdb file around this
region are fully correct? This kind of looks like a bug in ambpdb, since
it should not put a TER card in the middle of a residue. But if the prmtop
file is bad somehow, it could be fooled.

....dac

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