[gmx-users] OPLS force field issue

[Justin Lemkul]

On 4/30/15 11:28 AM, Mary Less wrote:
> Dear Justin,
> Thank you for your reply.
> I am trying to write an opls unied atom forcefield for Tetrahydrofuran (THF). I
> thought the common way to write a forcefield
> is to consider the atomtypes in the atomtypes.atp and choose those types which
> are suitable for the problem.
> (Considering things like the chemical surroundings as well as the charge to be zero)
> If I consider opls_071 for example I found the description "CH2 (SP3) ALKANES"
> which describes the chemical behaviour for
> my problem very well, as I think.
> I choosed opls_110 because of the description "United-atom Ether CH2 (-O)"
> because of the
> fact that the CH2 is bonded to an oxygen atom there as well.
> So do I just have to choose other atomtypes to build the united atom THF forcefield?
> What points do I have to take into account when choosing suitable atomtypes?
> Nevertheless I am wondering, that there are in general no bonding, angle or
> dihedral parameters for C2 given in the ffbonded.itp.
> (For example C2 and C3 or C2 with any arbitrary other atomtype)
> Does this mean that the type C2 is never bonded to any other atomtype?

More likely it's just a set of parameters that was never ported over.  The 
OPLS-UA force field is quite old, likely outdated at this point, but perhaps 
people are using it for something.  The OPLS-AA is more modern and more 
frequently used, so it is fully supported.  If there are missing parameters, 
either (1) those are the wrong types to use (sorry, can't help you there, and 
the documentation is rather cryptic) or (2) it's just something missing in the 
force field implementation that should be somewhere in the literature.

-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

==================================================