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

[Justin Lemkul]

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
>

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
>>
>> --
>> ==============================**====================
>>
>> 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
>>
>> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
>> (410) 706-7441
>>
>> ==============================**====================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>
>
>
>

-- 
==================================================

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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