[AMBER] Error due to faulty Connection atoms

From: Guillem Vila I Julià <guillem.vila.julia.upc.edu>
Date: Mon, 3 May 2021 12:11:25 +0200

Dear Amber users,

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.

I don't want to have any separation between the "new" residue bound to the
Retinal and the following residue (the THR that appear in the error), and I
have no idea how to solve this problem.

If anyone could help me solve it, I would really appreciate it,


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Received on Mon May 03 2021 - 03:30:02 PDT
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