AMBER Archive (2008)

Subject: Re: AMBER: misplacement of TER by leap

From: David A. Case (
Date: Mon May 05 2008 - 13:55:29 CDT

On Mon, May 05, 2008, Jena M wrote:
> After using leap to build the top and crd files I used ambpdb to obtain
> the corresponding pdb file. Strangely, leap puts a TER in the wrong place,
> separating residue 661:

If I understand correctly, it is ambpdb (not leap) that is putting the TER
card in the wrong place. Is that correct? Have you tried to use the savePdb
command in leap to create a pdb file?

Also, please look in the prmtop file, and find the section
"ATOMS_PER_MOLECULE". What are the first few numbers there?


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