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

[Alexander Alexander]

Thanks for your response.

What does "being compatible" mean here, please?

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?

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!?

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?

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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>