AMBER Archive (2007)

Subject: Re: AMBER: About TER records

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Nov 24 2007 - 15:34:59 CST

--- "David A. Case" <case_at_scripps.edu> wrote:

> On Fri, Nov 23, 2007, Francesco Pietra wrote:
> >
> > If I remember correctly, recent pdb rules tell that it is technically
> > correct to remove the TERs between HETATM residues because HETATM residues
> > in PDB format are not connected to each other unless there are CONECT
> > records that say the contrary.
>
> As far as I know, Amber's LEaP does not make the above distinction between
> ATOM and HETATM records. Patches are welcome, but I don't think it will be
> easy to implement this logic. I'm also cc-ing this to Wei Zhang, so that he
> can think about what sleap does.

My modest understanding is that TER records do well their job and, as far as
the entry to Amber (Leap) is concerned there is probably little scope to make
even more complex the language. Removing TERs implies putting CONECTs, I
believe (see, please, my separate mail on TER/CONECT. Though, there are other
aspects that may require complexity above pdb with TERs. If DOCK works with
mol2 files there are surely good reasons.

Thanks
francesco

>
> ...dac
>
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