SV: [gmx-users] g_saltbr

[Sarah Witzke]

Dear gmx users,

 

I'm sorry to continue an old thread - here's a summary:

I have a DMPC bilayer surrounded by water and a small organic molecule with a deprotonated carboxylic acid. The small molecule diffuses near the membrane interface/into the membrane. I would like to calculate any formed salt bridge between the negative carboxylic acid of the small molecule and the positive charge of the DMPC choline nitrogen. To do this I use these two commands:

g_saltbr -f zzz.xtc -s zzz.tpr -t 0.5 -b 100000 

g_saltbr -f zzz.xtc -s zzz.tpr -t 0.5 -b 100000 -sep

The first command I use to get the files min-min.xvg, plus-plus.xvg and plus-min.xvg. Here I am interested in plus-min.xvg to tell me which of the salt bridges between the small molecule and DMPC is between the negative acid and the positive choline (as opposed to between the negative acid and the negative phosphate of DMPC). 

Then I run the command again with -sep to get the individual graphs of each interaction. This is unfortunately a rather tedious exercise since very many files are generated for all sort of charged interactions (DMPC-DMPC, smallmolecule-smallmolecule, counterion-counterion, and pairs thereof), and then I have to select the wanted ones by looking through plus-min.xvg. I guess I could make some sort of script to make it easier, but I just want to check if there is absolutely no way to include an .ndx file or only choose plus-min interactions?

 

Another thing, when running the second command several of each files are generated, for instance:

sb-DMPC144:DMPC154.xvg

#sb-DMPC144:DMPC154.xvg.3#

Etc

The files are not identical when checked with "diff" or looked at in xmgrace.

I suppose the last generated files are the "correct" one, but what are all the other files?

 

Thank you in advance,

Sarah


________________________________

Fra: gmx-users-bounces at gromacs.org på vegne af Sarah Witzke
Sendt: fr 20-11-2009 14:55
Til: jalemkul at vt.edu; Discussion list for GROMACS users
Emne: RE: [gmx-users] g_saltbr






-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Justin A. Lemkul
Sent: Fri 20-11-2009 14:25
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_saltbr



Sarah Witzke wrote:
> Dear gromacs users,
>
> First of all thank you for all your previous help!
>
> I have a new question regarding an analysis of ionic interactions between
> DMPC lipids and a small molecule with a deprotonated carboxylic acid.
> g_saltbr takes as input an .xtc file and a .tpr file and from these files it
> measures the distance between all charged groups and create the three files
> min-min.xgv, plus-plus.xvg and min-plus.xvg. My bilayer contains 128 DMPC
> molecules each having a positively charge and a negative charge. The small
> molecule has one negative charge. Running g_saltbr -f xxx.xtc -s xxx.tpr -sep
> -b 100000 -t 0.5 puts the distances between charged atoms in separate files,
> which is what I would like. But now the files are named like this: sb-<small
> molecule>'number':DMPC'number'.xvg How can I then know whether the small
> molecule is interacting with a positive atom in DMPC (like plus-min) or a
> negative atom in DMPC (like min-min)?
>

If you omit the -sep option, you'll get plus-min.xvg, min-min.xvg, and
plus-plus.xvg.  In these, you will find the different groups that interact
through these different charge interactions.

OK.

> One more question is on the distance: From this mail I read that the distance
> calculated is between the charged atoms, not the COM of the charge group:
> http://lists.gromacs.org/pipermail/gmx-users/2005-June/015811.html Then what
> about my small molecule with the deprotonated acid? Here the charge of the
> oxygens is spread on both of then. As is also the charge on the
> DMPC-phosphate oxygens? How can it then be a distance between atoms, when the
> charge is spread over several atoms?
>

The program identifies the interacting charge groups within the cutoff
specified, and then prints the minimum distance between any two atoms in the
interacting charge groups, as stated in the thread you quote.

Ah, now I understand the comment. Slow Friday. Thank you!

-Justin

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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