[gmx-users] Protein-ligand simulation

[Justin Lemkul]

On 3/4/13 9:15 AM, Ankita naithani wrote:
> Hi,
>
> I recently ran a simulation with the complete structure of my protein
> alongwith the ligands. I was running some analysis and was trying out
> the Principal component analysis.
> I used the g_covar tool to get the eigenvalues and eigenvectors for
> protein back bone. However, when I try to use g_covar for the whole
> system, it shows me segmentation fault. My problem is that I want to
> see the simulation of my protein and ligand together as a whole. I ran
> g_covar individually for all the ligands and saw the first eigenvector
> movie in pymol and similarly for protein backbone. But I would really
> like to see the ligand and protein dynamics together because when I
> see the eigenvector individually, the ligand is moving in a direction
> probably towards the binding site and it would be quite helpful if
> anyone could suggest how can I possibly view them together.
>

Like any Gromacs tool, you can create an index group of whatever subset of atoms 
you would like to consider.  The segmentation fault when considering the whole 
system likely resulted in an exhaustion of available memory, which is not 
surprising given the size of the matrix.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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