[gmx-users] Trying to use AMBER parameters in GROMACS

[Crystal Vander Zanden]

Qinghua,

Thanks so much!  This worked beautifully!!!  I wish I had asked sooner
instead of struggling with these old broken codes.

I apologize for the accidental duplicate post that followed.

Thanks,
Crystal


>
> Message: 6
> Date: Wed, 3 Jan 2018 18:03:37 +0100
> From: Qinghua Liao <scorpio.liao at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Trying to use AMBER parameters in GROMACS
> Message-ID: <d60d70c8-9cfd-1377-7bb5-8766b3a4ba56 at gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Hello,
>
> You could try to build the system with AmberTools (it is free), choose
> the force fields available in Amber.
> Once you get the topology and coordinates files (prmtop and inpcrd), you
> can convert them into top and gro
> in Gromacs format with *parmed*. Then you can perform the simulations
> with Gromacs.
>
> import parmed as pmd
>
> #convert prmtop and inpcrd into top and gro
> amber = pmd.load_file('mol_sol.prmtop','mol_sol.inpcrd')
> #
> amber.save('mol_sol.top')
> amber.save('mol_sol.gro')
>
> You can google for more details.
>
>
> All the best,
> Qinghua
>
> On 01/03/2018 05:52 PM, Crystal Vander Zanden wrote:
> > Dear GROMACS Community,
> >
> > I am trying to parameterize my system using AMBER force fields, and then
> do
> > molecular dynamics with the GROMACS software.  I want to use the Lipid17
> > force field, which is not build into GROMACS.  Does anyone know of a way
> to
> > do this?
> >
> >
> > I have found 3 programs people have written to do this, but in short,
> none
> > of them work because the codes are too old (ca. 2003).
> >
> > 1) https://code.google.com/archive/p/amber2gmx/downloads
> > This would work, but it is written to use a command line parser package
> > that is too old and I can?t find (com.tsd.apps).
> >
> > 2) The amber2gmxrtp script build into GROMACS
> > This doesn?t work because it was written to take .in and .prep files
> (made
> > for the antiquated AMBER Prep program).  Those file types have been
> > replaced with .lib (made for Leap)
> >
> > 3)The amberconv.tgz package from the GROMACS website (
> > http://www.gromacs.org/Downloads/User_contributions/Other_software)
> > This was missing an include file when I tried to compile it.
> >
> >
> >
> > The reason for using AMBER force fields:  My system has lipids, protein,
> > and a small molecule - all of which can be well described with AMBER
> force
> > fields.  Since AMBER force fields are QM-based, it would be really easy
> to
> > parameterize the small molecule using Antechamber and low-level QM.
> > GROMACS force fields are empirically derived, so it will be much more
> > challenging to parameterize the small molecule in a way that?s consistent
> > with the rest of the force field for lipids and protein.  I plan on
> > simulating more small molecules in the future.
> >
> > I am hoping to use GROMACS because it's free, fast, and also not too
> > difficult to learn.
> >
> >
> > Thanks in advance for any advice you?re able to provide!!
> > Crystal
> >
>
>
>
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> End of gromacs.org_gmx-users Digest, Vol 165, Issue 14
> ******************************************************
>



-- 
Crystal M. Vander Zanden, Ph.D.
ASERT Postdoctoral Fellow (IRACDA)
University of New Mexico, Albuquerque