[gmx-users] RMSD analysis of protein-ligand complex

[Justin Lemkul]

On 10/5/19 1:58 PM, Quin K wrote:
> Thank you.
>
> I examined the trajectory using VMD and noted that ligand had come out of
> the binding site and is running around.
> How is this possible? I have used the guidelines in mdtutorials.com to set
> up the system.
> However it's worth noting that there was a power failure around the same
> time (23ns) and I had to restart MD with append command.
> Could this have had an affect on MD? Do I have to recreate trajectory file
> after restarting MD, instead of using the default trajectory?

I imagine it's possible that the power failure caused a corruption in 
some file, and it's too much of a coincidence that just when the power 
failed, your simulation changed radically. I would re-run it.

Also note that a ligand can dissociate from the binding site if the 
topology is not well parametrized, leading to insufficiently strong 
interactions. You shouldn't likely encounter such a problem if you get a 
reasonable CGenFF topology, but it's worth noting as a general problem 
with any ligand parametrization.

-Justin

> Regards
>
> On Sat, Oct 5, 2019 at 9:53 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 10/5/19 11:59 AM, Quin K wrote:
>>> Thank you.
>>>
>>> I got following when I analysed Ligand RMSD protein backbone as east
>> square
>>> fit.
>>> Graph <https://photos.app.goo.gl/JZJaLt1BxJi1qgwV7>
>>> Can you please comment why there's high fluctuation after like 23 ns?
>>> What could this mean?
>> Watch the trajectory and see what is going on. Make sure you've properly
>> re-imaged to account for PBC effects.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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