Hi Carlos
(Within cpptraj):
> parm 1i10_final.prmtop
[parm 1i10_final.prmtop]
Reading '1i10_final.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
> check 1i10_final.prmtop offset 1.0
[check 1i10_final.prmtop offset 1.0]
Warning: Action specified before trajin/ensemble. Assuming trajin.
CHECKSTRUCTURE: Checking atoms in mask '*', warnings output to STDOUT.
Number of problems in each frame will be saved to set '<1i10_final.prmtop>'
Checking for bond lengths > Req + 1.15 Ang
Checking for inter-atomic distances < 0.80 Ang.
Cutoff for building pair list is 4.000000 Ang.
This is where I'm not sure if I've either typed something wrong or it's worked and I'm not sure how to check the results (I couldn't find an example of it being used this way)
With regards to ParmEd, similarly couldn't find anything on Jason Swails' github describing how to list present bonds.
Loading prmtop and then inpcrd files into VMD didn't seem to work either, again maybe performed erroneously by me
Thank you for the help
Sam
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________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Wednesday, January 13, 2021 12:37:09 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] LEaP Error/questions.
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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