yes, but the 2.0 is the deviation from the reference bond length, not
actual bond length. I would probably just go with the default offset.
On Wed, Jan 13, 2021 at 9:39 AM Sam Walsworth (Researcher) <
Sam.Walsworth.hud.ac.uk> wrote:
> 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?
>
> Get Outlook for Android<https://aka.ms/ghei36>
>
> ________________________________
> 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
> >
> >
> > Get Outlook for Android<
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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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Received on Wed Jan 13 2021 - 07:00:03 PST
