AMBER Archive (2004)

Subject: Re: AMBER: averaged structure with unknown elements

From: Bill Ross (
Date: Wed Feb 25 2004 - 15:49:40 CST

> After averaging a structure from the MD trajectory in PDB format,
> I loaded this structure into xleap to make top and crd files for
> energy minimization. When I was loading pdb file into xlaep, I got
> a message "leap added 2594 missing atoms according to residue
> templates: 2584 H/lone pairs, 10 unknown element". But I could save
> the prmtop and inpcrd files for this structure without complaints.

What program did you average with? Did you do anything to
the pdb before loading? It sounds like you may have removed
H and other atoms, and leap replaced them as best it could,
which may or may not result in a different structure.

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