Re: [AMBER] Problem with covalently bonded ligand parametrization

From: David A Case <>
Date: Sat, 23 May 2015 12:45:27 -0400

On Sat, May 23, 2015, Gustavo Avelar Molina wrote:

> I get a lot of messages like:
> Added missing heavy atom: .R<NTRP 254>.A<O 26>

This means that the Amber residue library for N-terminal TRP is expecting an
atom named "O", but that is missing from your input PDB file. You need to see
if this is expected, or if it means that something is wrong.

> At the end, I receive this message:
> Bond: Maximum coordination exceeded on .R<ACR 223>.A<H6 31>
> -- setting atoms pert=true overrides default limits
> ATOMS NOT BONDED: .R<ACR 196>.A<C5 12> .R<ACR 223>.A<H6 31>

Something is surely wrong here, but we would need a lot more information
about how how tried to make your modified residue to be of any help.

Tutorial B5 shows an example of how to set up a simulation with a covalent
protein modification. Make sure you understand what is going on there
(especially since you say you are new to Amber.)


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Received on Sat May 23 2015 - 10:00:03 PDT
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