[gmx-users] MD on protein-RNA complex

[Justin Lemkul]

On 3/7/15 1:05 AM, Brett wrote:
> Dear Justin,
>
> If my protein-RNAcomplex also contains acetyl-tRNA, can the current force fields
> of the gromacs covers both protein, RNA, and acetyl-tRNA? Will I meet difficulty
> with pdb2gmx when I create the input file for complex containing protein, RNA
> and acetyl-tRNA?

Probably.  Modified base parameters may exist (or can be easily made for 
something like this) but are unlikely to be included in the official force 
fields.  Refer to the .rtp files to know if something is there or not.

-Justin

-- 
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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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