On 8/19/14, 4:17 AM, Natalie Stephenson wrote:
From: [email protected]
[[email protected]] >on behalf of Justin Lemkul
[[email protected]]
Sent: 18 August 2014 17:47
To: [email protected]
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
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to [email protected].
--
==================================================
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
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to [email protected].
