[gmx-users] Generate diagram/figure with information about protein-ligand interactions

[Justin Lemkul]

On 3/31/16 6:58 AM, bio hpc wrote:
> My problem is not excel or whatever graphical program. I just need the data,
> in an automatic way. Then I can use either matplotlib or similar to get the
> plots automatically. But my question is if there is somewhere a repository of
> gromacs scripts with a script doing an analysis of the protein-ligand
> itneractions during trajectory. I do not think to be the only one requesting
> this
>

I doubt you can do something like this "automatically," though of course it 
could be done.  My hesitation comes from the fact that the terminology used is 
quite generic and could be defined several ways.  Without knowing the context of 
the figure (which I assume is pulled from a paper, in which case your questions 
should be directed to the authors, not here...) then it's hard to say.  Of 
course GROMACS tools will do analysis like this (gmx hbond, gmx mindist -on, gmx 
saltbr) but you'll have to mine those data appropriately to pull out whatever is 
useful to you.

-Justin

>
>> El 30/3/2016, a las 6:46, Sun Iba <sun.iba2 at gmail.com> escribió:
>>
>> i am sorry, i replied prior to looking at your figure. Actually, i have
>> never came across plotting data in this matter. However, I believe you
>> have tabulated data, so you can use Origin or excel for generating similar
>> images. You need little effort to arrange the data in desired manner. Best
>> Wishes
>>
>> On Wed, Mar 30, 2016 at 3:15 AM, bio hpc <biohpc2015 at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> after a protein-ligand simulation with gromacs, I would like to be able
>>> to generate a diagram/figure with information about protein-ligand
>>> interactions, something like this:
>>>
>>> https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg <
>>> https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg>
>>>
>>> I had a look to all gromacs tools but found nothing similar to this.
>>> Where can I start from?
>>>
>>> Thanks,
>>>
>>> biohpc
>>>
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>
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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