[gmx-users] g_dist as an alternative for g _saltbr

[Diogo Martins de Sá]

Dear Justin,

thanks for your reply. To start with, here are the links where you
mentioned "looping calculations"
(http://article.gmane.org/gmane.science.biology.gromacs.user/59569/match=g_saltbr+looping+calculations)
and "track persistence of interactions"
(http://www.researchgate.net/post/Can_anyone_help_with_salt_bridges_with_gromacs)

Since g_saltbr is dumb in its main function (and should actually be
called something like g_electrostaticInteractions), I've decided to
tackle this question in the following manner:

1. I must use gromacs in way where I find all the SBs in my system, and
just those.
2. I must use gromacs to observe the distance of these SBs as a function
of time.

This is how I intend to do it.

1. Acording to Kumar & Nussinov 2002 (Close-Range Electrostatic
Interactions in Proteins), salt bridges must have at least a pair of
sidechain functional-group nitrogen and oxygen atoms within 4 ä
distance. So I will use g_select to create groups of ASP's & GLU's
sidechain Oxigen and respective hydrogens and HIS's, Lys's & Arg's
sidechain Nitrogen atoms and respective hydrogens. Why include the
hydrogens? Because I'll need them to use g_hbond. Why use g_hbond?
Because of the matrix. Why is the matrix so important? Because of your
(Justin's) script that shows the percentage of time that a given
hydrogen bond existed during the trajectory:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html.
So I will run g_hbond with -r 0.49 (0.35 from hydrogen bond + 0.14 which
is the furthest distance a covalently bonded hydrogen can be from
nytrogen, this distance is 0.12 for oxigen. Hydrogen bonds pull the
covalently bonded H away from atoms and this is directly proportional to
the strengh of the bond). After this process, I will have all the salt
bridges and the percentage of their appearence through the trajectory
(thanks to your script). So I now I know which ones I should take a
closer look.

2. To measure distance as function of time, I can use either g_bond
(with -d) or g_dist. If I get few SBs after step 1, I will use g_dist,
because then I will make individual groups. If I get more than a few
SBs, g_bond can organize each one and I have to make only two groups. 


What do you (and any other user reading) think about this strategy?

I do have one problem, I never used g_select and I'm having some
difficuly understanding the syntax. Does any one know how I should call
g_select so I create index groups like I mentioned in step 1??

Regards,

Diogo


-------------------------------------------------------------------------------------

Date: Wed, 15 Oct 2014 16:22:22 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] g_dist as an alternative for g_saltbr
Message-ID: <543ED77E.3060600 at vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed



On 10/15/14 2:19 PM, Diogo Martins de S? wrote:
> Fellow users,
>
>
> I have read several emails exchanged in this discussion list where
> g_dist is presented as a better choice for observing salt bridges in the
> trajectory. And I'm totally inclined to agree with that, but that would
> be the case where you already know which are the SBs present in the
> system. If one has this information, he could easily create groups of
> individual residues (which would actually contain just the ionazable
> atoms and their hydrogens, depricating the carbons and other atoms) and
> observe how the salt bridges behave.
>
>
> My question is concerning the situation where you still don't know which
> are the salt bridges in the system and, after that, which are the ones
> you should take a closer look (I think the obvious approach would be to
> search literature, but that is not always successful).
>
>
> Justin Lemkul has mentioned, in two diferent discussions, using g_dist
> to "track persistence of interactions" and "looping calculations" to
> address the situation I've just mentioned.
>
>
> Could someone elaborate on those? I am confused as to what they actually
> mean and how to proceed (especially in the case of "looping
> calculations").
>

Likely I was referring to looping over calls to g_dist (in the future,
please 
link to any previous discussions - it's hard for me to keep track of all
of the 
thousands of messages I've sent :)

One can certainly use g_saltbr to look at positive-negative interactions
en 
masse, but it's a fairly "dumb" program, in that it considers a huge
amount of 
groups that don't matter. You can weed through all of that to find
things that 
might be of interest.

-Justin

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

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

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