AMBER Archive (2008)

Subject: Re: AMBER: PDB files in Amber10

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Mon Aug 25 2008 - 16:32:16 CDT

Hi,

On Sat, 2 Aug 2008, Francesco Pietra wrote:

> I had problems in the past (solved with your help) in getting pdb
> files from other programs (Chimera, Modeller, that I use in the chain
> modeling/docking/md) compatible with Amber9.
>
> Now I am planning to do that sequential computing with Amber10, which
> I already used in continuing work with files from Amber9. Having now
> to set up files from scratch, may I ask if there is any difference
> with respect to the layout of pdb files with respect to Amber9? In
> particular:
>
> --- Four-character atom names.
>
> --- Need/no-need of "TER" line to separate chains (which end with a
> HETATM line for an halide anion, belonging as ligand to the same
> chain).
>
> --- Better to group each HETATM line at the end of all chains?
>

Amber 10 is the same as Amber 9, but
some programs/files in AmberTools have been updated
to accept the new version 3.0 pdb files:
leaprc.ff99bsc0
nab components with -wwpdb option; see AmberTools.pdb
reduce

But i havent checked these vis-a-vis your items above; see
http://www.wwpdb.org/docs.html

Scott

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu