[gmx-users] regarding pdb

[Justin Lemkul]

On 7/13/14, 7:52 AM, pratibha kapoor wrote:
> Hi,
>
> I would like to simulate apo form (without metal ions) of my protein for
> which no pdb is available.
> Would it be correct if I just remove the metal ions manually from the
> metallated pdb file and then simulate?
>

Provided you simulate for adequate time to allow for whatever the necessary 
structural rearrangements are, it's a reasonable approach.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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