[gmx-users] extracting from TRR

niyaz.sabir niyaz.sabir at gmail.com
Fri Sep 26 21:16:44 CEST 2014

Dear Justin,

Thank you very much for your respond. It seems however my poor English put 
me in a spot again.
I do not need to find the lowest RMSD frame from a trajectory, it is too 
simple even for such a dummy as I am.
I need to find a frame that has lowest RMSD regarding to another .pdb file. 
In other words, I wish to compare the similiraty of two pdb structures:
Structure A (I called it reference protein) and structure B (is to be 
extracted from md.trr). Structure B will not necessarily posses the lowest 
RMSD. The process of extracting the needed frame should be automatic.
I inclined to think playing with g_confrms could help, but I do not know 
how. Help, please.



----- Original Message ----- 
From: "Justin Lemkul" <jalemkul at vt.edu>
To: <gmx-users at gromacs.org>; <niyaz.sabir at gmail.com>
Sent: Friday, September 26, 2014 9:27 PM
Subject: Re: [gmx-users] extracting from TRR

> On 9/26/14 6:42 AM, N. S. wrote:
>> Dear GMX experts,
>> How could I extract the only state from MD-simulation .TRR (or traj.xtc)
>> file that has the lowest RMSD from the reference protein.pdb file?
>> Please give me a line of code in UBUNTU or the script.
> Calculate the RMSD using g_rms, find the minimum value, then extract that 
> frame with trjconv -dump.
> -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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