Hi Juliette,
If you want a true vacuum simulation, then don't add water and just build
it without the solvate command. The vacuum environment is quite different
from solution, though, so you might want to think about whether this is a
good match for what you want to learn about self-assembly (unless you truly
want to study it in vacuum, like in the gas phase).
carlos
On Fri, Nov 12, 2021 at 7:40 AM Juliette Newell <
juliette.newell.postgrad.manchester.ac.uk> wrote:
> Hi Carlos,
>
> Thank you for getting back to me. Is there an alternative command to use
> instead of solvateoct?
>
> Best wishes,
> Juliette
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: 12 November 2021 12:37
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Running Simulations in a Vacuum
>
> your leap script adds water (solvateoct), so this isn't set up for
> vacuum simulations.
>
> On Fri, Nov 12, 2021 at 7:34 AM Juliette Newell <
> juliette.newell.postgrad.manchester.ac.uk> wrote:
>
> > Dear Sir/Madam,
> >
> > I am currently using the amber MD software to run simulations looking at
> > peptide self-assembly.
> >
> > I am trying to run a simulation in a vacuum, however when I get to the
> > equilibration step I get the error:
> >
> > 'Error: ifbox=2 in prmtop but angles are not correct'
> >
> > My tleap script is:
> >
> > source leaprc.gaff2
> >
> > source leaprc.protein.ff14SB
> >
> > source keaprc.water.tip3p
> >
> > CDPA = loadmol2 CDPA.mol2
> >
> > loadamberparams CDPA2.frcmod
> >
> > saveoff CDPA2.lib
> >
> > loadoff CDPA2.lib
> >
> > solvateoct CDPA CDPA 25
> >
> > check CDPA
> >
> > saveamberparm CDPA CDPA2.top CDPA2.crd
> >
> > Are you able to suggest why I may be getting the error?
> >
> > Best wishes,
> > Juliette
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Nov 12 2021 - 07:00:02 PST
