AMBER Archive (2006)

Subject: Re: AMBER: help with leap

Date: Thu Aug 17 2006 - 09:46:07 CDT

Hi Seth,

I advise you to go through the AMBER tutorial 1
( and generate your
structure with nucgen.
I read your attached pdb file and it seems like you did not use the
“AMBER” atoms naming convention for nucleic acids.


> Dear Amber Community,
> I have created a nucleic acid structure in pdb format using another
> program.
> The stucture "looks" fine in other viewers but in xleap there appear to be
> many
> extra unconnected atoms. I have attached a copy of the pdb file... in
> hopes
> someone may kindly take a quick look at it.
> Thanks,

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