[gmx-users] Query

[Justin Lemkul]

On 5/19/15 1:15 PM, Priya Das wrote:
> Yes Justin...i watched the dynamic structure carefully. As it is a
> transmembrane protein it is stringently moving.
> The dynamic movement of the structure seems fine.
> I used the backbone of protein for calculating Rmsd.

Consider everything else I said.

> I also want to know the ligand stability, for it i need to check the least
> square fit of ligand , right?

There are many ways to assess this.  RMSD is just one possible metric.

-Justin

> On May 19, 2015 5:11 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 5/19/15 6:29 AM, Priya Das wrote:
>>
>>> Dear all,
>>>
>>> While generating RMSD plots of protein in presence of ligand, i am getting
>>> a RMSD of around 4.5 Angstrom around 10 ns after which the system is
>>> almost
>>> stable.
>>> Is it an acceptable RMSD?
>>> What is the acceptable range for RMSD for structures?
>>>
>>>
>> There is no general rule, and a number without context is meaningless.
>> How did you calculate the RMSD - backbone? heavy atoms? all atoms?  Does
>> your protein have a lot of variable loops, and did you consider these?  Or
>> did you just consider structured parts of the protein?  Did you include
>> termini?  Did you watch the trajectory to see what's happening?
>>
>> -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
>>
>> ==================================================
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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

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