AMBER Archive (2002)

Subject: Re: TIP4P

From: David Case (case_at_scripps.edu)
Date: Fri May 31 2002 - 09:44:19 CDT

On Fri, May 31, 2002, SEKIJIMA Masakazu wrote:

> > pep = Loadpdb pep.pdb
> Loading PDB file: ./pep.pdb
> Created a new atom named: H within residue: .R<NALA 1>
> Added missing heavy atom: .R<CALA 3>.A<OXT 11>

Watch carefully for messages like the above; this means that there are
atoms in your pdb file (the H atom in the first residue) that LEaP does
not know about. You need to fix this before proceeding.

You can use the "desc" command to see the atoms that LEaP thinks should
be there.

In this particular case, the hydrogens at the N-terminal residue of a
peptide are called H1, H2, H3.

I would recommend getting some experience with "regular" simulations (e.g.
with TIP3P water) before trying less commonly used options.

...good luck...dac 

-- 

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