[gmx-users] Force Field for amino acid and peptide

[Mark Abraham]

Hi,

On Fri, May 27, 2016 at 12:55 PM Alexander Alexander <
alexanderwien2k at gmail.com> wrote:

> Thanks for your response.
>
> What does "being compatible" mean here, please?
>

That someone has done a bunch of work and presented results that show that
sets of parameters reproduce physically meaningful things. Then others read
it, argue about it, fix it, or cite it. :-) #science


> Actually, the FF of the surface (meanly \sigma and \epsilon in L-J) was
> harvested via a series of parametrization of some parameters with the
> quantum calculation of the same parameters. So, how can I find the most
> compatible FF of the peptide with this surface then?
>

Either someone has done some similar work that you can read and learn from,
or they haven't. In the latter case, you can make some stuff up and likely
not publish, or be prepared to find some data you can hope to reproduce,
and then work out a protocol to reproduce it.

I just chose "OPLS-AA" force field for peptides because the [ defaults ]
> sections (in topol.top) for "OPLS-AA" FF (among the FF provided in Gromacs)
> was quite close to the [ defaults ] section of my simulations for the
> surface. But, I really do not know how reliable this is!?
>

It isn't reliable until you can say why it is :-)


> I could not see the CVFF force field in the suggested list of FF in "gmx
> pdb2gro peptide.pdb ...", so, I was wondering how can use CVFF force field
> for peptides in this simulation?
>

If GROMACS already implements the necessary functional forms, then it's a
matter of someone who wants it to work converting the input files for the
force field.

Mark

Thanks.
> Best regards,
> Alex
>
>
>
>
> On Thu, May 26, 2016 at 3:03 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 5/25/16 11:05 AM, Alexander Alexander wrote:
> >
> >> Dear Gromacs user,
> >>
> >> I am going to simulate the binding free energy of some amino acid to a
> >> metal surface in aqueous solution and also peptide adsorption behavior
> >> into
> >> this surface.
> >>
> >> I know the force field of the surface as well as the better type of
> water
> >> for such a work, but I do not know which type of Force Filed could be
> the
> >> better choice for the peptide (amino acids) for this simulation, so I
> >> would
> >> be so appreciated if anybody could address me to a better choice of
> >> peptide
> >> (amino acid) Force Filed for such a goal?
> >>
> >>
> > One that is compatible with the force field of the surface.  A force
> field
> > is a self-consistent entity.  In general, you can't mix and match
> different
> > parameter sets from different sources, unless those parameter sets have a
> > common origin or shared method of parametrization.  So your choice here
> for
> > treatment of the protein really isn't a free one, it's not about being
> the
> > "better choice" for the system; there can be only one answer, if it
> > exists.  Maybe there is no protein force field compatible with whatever
> the
> > surface is.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
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