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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>
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Received on Fri Nov 12 2021 - 05:00:03 PST
