Re: [AMBER] Tleap-complex PDB problem

From: Rui Chen <>
Date: Wed, 27 Nov 2019 09:52:12 -0700

Dear David,

Thank you for your reply. Have a nice day.

Best regards,

On Wed, Nov 27, 2019 at 9:43 AM David A Case <> wrote:

> On Wed, Nov 27, 2019, Rui Chen wrote:
> >
> >Thank you for your help, I solved the problem. I have a simple question,
> in
> >tleap.log file almost for all the residues I can see "(Residue 2: ILE,
> >Nonterminal, was not found in name map.)" But in leap itself (from
> >terminal), I could not see this sentence. I found in the previous mailing
> >list, people have similar questions. Should I do something or I don't need
> >to worry about this?
> Don't worry about this: we will probably finally remove this message
> from the leap.log file with the next release.
> FWIW: "Nonterminal" means that residue 2 is in the middle of the chain,
> and is not an N-terminal or C-terminal residue.
> "not found in name map" means that ILE was not renamed to something else
> via a PdbResMap entry.
> Neither one of these facts is (generally) of the slightest interest to
> anyone. This message was coded in about 1990, when tleap was very new
> (so people wanted to follow what is was doing) and proteins being
> simulated had maybe a hundred residues. By now, it's just noise that
> makes the leap.log file much less helpful to users. The camel's back
> for me came when a built a system with about 70,000 residues.
> ....dac
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Received on Wed Nov 27 2019 - 09:00:02 PST
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