Re: [AMBER] Tleap-complex PDB problem

From: David A Case <>
Date: Wed, 27 Nov 2019 11:42:31 -0500

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.


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Received on Wed Nov 27 2019 - 09:00:01 PST
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