[gmx-users] Most appropriate structure to compare to in g_rms

[Justin Lemkul]

On 8/19/14, 4:17 AM, Natalie Stephenson wrote:
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] >on behalf of Justin Lemkul [jalemkul at vt.edu]
>> Sent: 18 August 2014 17:47
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Most appropriate structure to compare to in g_rms
>
>> On 8/18/14, 9:41 AM, Natalie Stephenson wrote:
>>> Hi all,
>>>
>>> This probably seems a really obvious question, but I'm struggling to get my
>>> head around it. I am performing simulations to determine the effect of
>>> mutations on key regions of the protein. I have a crystal structure which I
>>> am using as the WT construct, and have performed homology modelling to create
>>> the point mutations of interest.
>>>
>>> I have used g_rms using the Production MD .tpr as the reference to look at
>>> the change in movement for key regions of the structure, comparing the degree
>>> of movement with the WT and mutated construct. Unfortunately, this does not
>>> necessarily tell me about changes occuring, for example, one key region is
>>> showing no change in RMSD however is displaced compared to that in the WT.
>>
>> Can you provide your exact command(s) and the groups chosen for fitting and
>> output?  The outcome is highly dependent upon proper choices being made.
>>
>
> The commands I have been using are:
> 1. g_rms -s prodMD.tpr -f prodMD.xtc -n index.ndx -tu ns -o prodMD_RMSD.xvg (to compare to equilibrate structure)
> 2. g_rms -s EM.tpr -f prodMD.xtc -n index.ndx -tu ns -o prodMDtoEM_RMSD.xvg (to compare to crystal structure)
>
> In both cases I have been chosing protein for the least square fit and then the specific region for the fit, though I'm not sure this is correct. What is the best way of knowing which is the proper choice for this? Is there any good resources I could access to read up on this?
>

Fitting to the entire protein is a bit uncommon; fitting is almost always done 
to backbone or C-alpha groups, because for a well-folded protein, the structure 
should not change a whole lot.  If you fit to the whole protein, you're trying 
to fit against rapidly moving side chains, especially those on the surface whose 
motions are not necessarily functionally significant and may actually obscure 
detail.

-Justin

>>> Would it be better to use the WT EM.tpr as the reference structure for
>>> everything (i.e. compare everything to the WT crystal structure)? Obviously
>>> these topologies will have slightly different numbers of atoms etc. will this
>>> be a problem?
>>>
>>
>> This will be a problem.  You can get around it, though, by using tpbconv (gmx
>> convert-tpr in 5.0) to extract just backbone atoms from both .tpr files and
>> trajectories.  If you don't, g_rms will complain about mismatching atom numbers
>> or you will be mapping the wrong atoms in the trajectory since the two proteins
>> have different numbers of atoms.
>>
>> Also note that g_rmsf is probably useful here, too, as you can get per-residue
>> fluctuations and RMSD.
>>
>> -Justin
>>
>
> This is what I had thought - I'll definitely try using tpbconv to fit the backbones and look into changes. Though some of the changes I am interested in are the sidechain movements. I'll definitely try the g_rmsf for this.
> Thanks so much for all the help!
>
> Natalie
>
>> --
>> ==================================================
>>
>> 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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-- 
==================================================

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

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