Re: [AMBER] LEaP Error/questions.

From: Sam Walsworth (Researcher) <"Sam>
Date: Wed, 13 Jan 2021 12:30:36 +0000


Sorry to bother again but I can't seem to get either cpptraj to list the long bonds in my topology or parmed to list bonds present
From: David A Case <>
Sent: 12 January 2021 13:21
To: AMBER Mailing List <>
Subject: Re: [AMBER] LEaP Error/questions.

On Tue, Jan 12, 2021, Sam Walsworth (Researcher) wrote:
>One small final thing: When I used the saveamberparm command, LEaP warned
>me there were bonds formed that were between 3 and 16 angstroms long
>(Warning: there is a bond of ... angstroms between:) but didn't specify
>where these bonds were located/which atoms connected.

Run the "check" command in cpptraj: it will identify long bonds for you.
(The fact that tleap is missing the identifiers has been fixed in the
development version, and will be a part of AmberTools21.)

You certainly should not ignore this.

...good luck....dac

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Received on Wed Jan 13 2021 - 05:00:01 PST
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