[gmx-users] addition of an isopeptide bond and its simulation

[Justin Lemkul]

Please do not reply to the entire digest, and remember to use an appropriate 
subject line.

On 4/25/17 1:47 PM, Raag Saluja wrote:
> Thank you, Justin! I will definitely try this out. However, I can't find
> anyone or any paper where they have done a similar thing... Could you
> please suggest which force field should be the best to try first?

Surely someone has done something reasonably similar, even if it's not the same 
thing.  If not, or you just can't find it, consider force fields generally and 
see who has the best parameters for the types of chemical group your addendum 
has.  Then consider your ability to assign a suitable topology, either by 
analogy or be de novo parametrization, depending on what's already available.

-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

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