can you copy/paste the command you gave and the output you got?
On Wed, Jan 13, 2021 at 7:30 AM Sam Walsworth (Researcher) <
Sam.Walsworth.hud.ac.uk> wrote:
> Hello
>
> 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 <david.case.rutgers.edu>
> Sent: 12 January 2021 13:21
> To: AMBER Mailing List <amber.ambermd.org>
> 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 - 05:00:02 PST
