[gmx-users] Calculating the distance between protein and ligand during ligand diffusion out of the box

[Trayder Thomas]

With a ligand diffusing as freely as I'm assuming (you've omitted a lot of
info, box size etc.) you aren't going to get PBC to play nice, although
-nojump should have atleast given you a different wrong answer.

Centering the system on the same point you are using to define the binding
pocket (may require custom index groups) should get you something more
reasonable looking.

Also, it depends on the size of your protein and what you're doing but you
should consider if it's even relevant whether the ligand is 2nm away or 5?

-Trayder



On Tue, Oct 8, 2013 at 6:53 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/7/13 1:39 PM, bipin singh wrote:
>
>> Thanks for the reply Dr. Justin.
>> I have also thinking of the same possibility but to further confirm, I am
>> sending the link for the plot of the distance between the COM of ligand
>> binding pocket and COM of ligand molecule, please find some time to have a
>> look at the plot and let me know if it seems a feasible behaviour during a
>> simulation.
>>
>> http://researchweb.iiit.ac.in/**~bipin.singh/plot.png<http://researchweb.iiit.ac.in/~bipin.singh/plot.png>
>>
>>
> Looks like nothing more than random motion to me.  Since you haven't told
> us what you're doing (unrestrained MD? pulling?), it's hard to comment
> further.
>
> -Justin
>
>
>  On Mon, Oct 7, 2013 at 8:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 10/7/13 10:46 AM, bipin singh wrote:
>>>
>>>  Hello All,
>>>>
>>>> I have calculated the distance between the binding pocket of protein and
>>>> the ligand molecule but due to ligand diffusion out of box, I am getting
>>>> wrong distance as first it increases till 5nm and then decrease again to
>>>> around 1nm during the simulation (which is not possible).
>>>>
>>>> I have fitted my trajectory with using trjconv -pbc mol -ur compact
>>>> -center
>>>> (protein) option.
>>>>
>>>> I have also tried the -nojump option but getting the same results for
>>>> distances.
>>>>
>>>> Please suggest how to get the real distance without the PBC effect.
>>>>
>>>>
>>>>  It sounds like that very well could be the real distance.  If the
>>> ligand
>>> diffused out, it simply becomes part of the solvent around the protein
>>> and
>>> can diffuse around freely.
>>>
>>> -Justin
>>>
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> ==============================**====================
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>
> Justin A. Lemkul, Ph.D.
> 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
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> 706-7441
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