Re: [AMBER] Error due to faulty Connection atoms

From: David A Case <>
Date: Wed, 12 May 2021 09:11:24 -0400

On Mon, May 03, 2021, Guillem Vila I JuliÓ wrote:
>I am trying to prepare a simulation of rhodopsin receptor. I have
>parametrized the residue bound to the Retinal but when i perform the LEaP,
>I get the following error:
>Comparing atoms
> .R<RET 297>.A<C14 64>,
> .R<RET 297>.A<H28 66>,
> .R<RET 297>.A<H29 67>, and
> .R<RET 297>.A<H30 68>
> to atoms
> .R<RET 297>.A<C14 64>,
> .R<THR 1>.A<N 1>,
> .R<RET 297>.A<H28 66>, and
> .R<RET 297>.A<H29 67>
> This error may be due to faulty Connection atoms.

Sorry for the delay in replying.

We are going to need more information. Can you create a small system, just
a few residues, that has the retinal bound in the way you want? We would
need to have the input retinal library, the input pdb file, and the exact
commands given to LEaP. Reproducing the error is a necessary first step


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Received on Wed May 12 2021 - 06:30:04 PDT
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