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

[Justin Lemkul]

On 4/25/17 12:42 AM, Raag Saluja wrote:
> Hi!
>
>  I need to study the effect of post-translational modifications on the
> biophysical properties of my protein. This involves the addition of an
> isopeptide bond to the primary chain of the C-terminal tail.
>
> How may I add this isopeptide bond? And then which force field can I use to
> simulate it?
>

Add the terminal residue as a new entity in the force field 
(http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field) 
and choose "None" as the C-terminus when processing with pdb2gmx so additional 
patching isn't attempted on that residue.  The force field you choose depends on 
which one is most straightforward to you for doing the parametrization or that 
has been demonstrated to handle similar cases well.

-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

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