AMBER Archive (2008)

Subject: AMBER: PDB files in Amber10

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Aug 02 2008 - 02:21:58 CDT

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?

In addition, since the anion in my protein acts as a specific ligand,
I guess parameters for it should be provided. I used in the past for
proteins with organic ligands the force fields ff99SB/GAFF. In view
that there will be also organic ligands (from Dock6), for which I want
to use GAFF, should the above halide-ion ligand receive parametrs from
which source?

Thanks
francesco pietra
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