I'm not sure exactly what you're doing in the script, but it looks like
you're solvating CDPA with other copies of CDPA. if that's your goal, it
might work, though the *packmol program *might be a more useful option. if
you want to try using the one build by leap, then it would be helpful to
see the full output from the MD run that gave the error.
On Mon, Nov 15, 2021 at 6:43 AM Juliette Newell <
juliette.newell.postgrad.manchester.ac.uk> wrote:
> Hi Carlos,
>
> I am hoping to run a simulation of 20 + non standard amino acids in a
> vacuum to study their properties after self assembly.
>
> So my issue is when loading the mol2 files into tleap, I am unsure how to
> load multiple.
>
> Thanks for pointing out the typo, I will amend that.
>
> Best wishes,
> Juliette
>
> Get Outlook for Android<https://aka.ms/AAb9ysg>
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Monday, 15 November 2021, 11:19
> To: AMBER Mailing List
> Subject: Re: [AMBER] Running Simulations in a Vacuum
>
> 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 - 13:00:03 PST
