So if I ran:
> parm 1i10_final.prmtop
> loadcrd 1i10_final.inpcrd
> check 1i10_final.inpcrd offset 2.0 (check for bonds longer than 2.0 ang)
> run
Or is there a way to combine the top/coord and run together?
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________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Wednesday, January 13, 2021 2:13:08 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] LEaP Error/questions.
as it says, you need to load coordinates first. It can't check for long
bonds without coordinates. You can trajin your coordinates from leap.
On Wed, Jan 13, 2021 at 8:28 AM Sam Walsworth (Researcher) <
Sam.Walsworth.hud.ac.uk> wrote:
> 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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