[gmx-users] Peptide orientation

[Justin Lemkul]

On 2/9/14, 9:33 AM, pratibha wrote:
> Dear gromacs users
>
> I have two peptides with their initial conformation as beta strand each. I
> have to place them laterally in antiparallel fashion before I can begin my
> simulation. I am aware that the random placement that can be done by ci
> option of genbox.
> But how to place peptides in specific orientations at specific distances.

Within Gromacs, the best options are editconf features like -rotate and 
-translate.  If you align one peptide along an axis (i.e. x-axis with editconf 
-princ), the remaining transformations are trivial.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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