[gmx-users] how to superimpose protein in frames?

[Justin Lemkul]

On 6/12/15 8:37 AM, Albert wrote:
> Hello:
>
> I am just wondering is it possible to superimpose the protein backbone in each
> frame? I try to do this by command:
>
> trjconv -f md.xtc -s md.tpr -pbc res -center
>
> when it pop up options for center, I select "backbone". However, when I
> visualize it in VMD, the protein in trjaceotry is not superimposed at all.....
>

trjconv -fit

-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

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