Hi Juliette,
what do you mean by the same number of molecules? It isn't clear what
you're trying to set up in your simulation.
also note that your script has a typo "keaprc" which probably should be
"leaprc"
On Mon, Nov 15, 2021 at 6:16 AM Juliette Newell <
juliette.newell.postgrad.manchester.ac.uk> wrote:
> Hi Carlos,
>
> Without using the solvateoct command (solvateoct CDPA CDPA 25) how would I
> be able to get the same number of molecules in the simulation?
>
> Thank you for your help.
>
> Best wishes,
> Juliette
>
> Get Outlook for Android<https://aka.ms/AAb9ysg>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Friday, November 12, 2021 2:32:48 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Running Simulations in a Vacuum
>
> 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
> > >
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Received on Mon Nov 15 2021 - 03:30:03 PST
