[gmx-users] MG-ATP

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 29 20:25:32 CEST 2011

Sajad Ahrari wrote:
> thanks felix
> you are right.both exist.but how can i tell gromacs to put MG ions in 
> the standard vicinity of ATP? or maybe gromacs knows it already and i 
> have to just type "MG-ATP" instead of "ADP"?

If all residues, including ligands and cofactors, exist in the .rtp database, 
all you need to do is run the structure through pdb2gmx and it will produce a 
topology.  Note that the presence of .rtp entries is a key caveat; pdb2gmx isn't 
magic and won't work for anything you provide as input.  But in the case that 
everything is in place for a given force field, then there should be no problem.

Try it and report back with specific errors if they arise.  Spending too much 
time on the hypothetical gets nothing accomplished :)


> ------------------------------------------------------------------------
> *From:* "Rausch, Felix" <frausch at ipb-halle.de>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Wed, April 27, 2011 1:33:52 PM
> *Subject:* [gmx-users] MG-ATP
> Hi.
> Looking at the list of building blocks available in GROMACS 
> (http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks?highlight=building+blocks) 
> you can find ATP as well as MG. So having a ATP-MG-complex in your 
> simulation shouldn't be a problem.
> Regards,
> Felix
> ------------------------------------------------------------------------
> *Von:* gmx-users-bounces at gromacs.org im Auftrag von Sajad Ahrari
> *Gesendet:* Mi 27.04.2011 10:52
> *An:* gromacs user forum
> *Betreff:* [gmx-users] MG-ATP
> dear users
> is "MG-ATP" known to gromacs ? in my pdb structure I have ADP and MG, 
> apart from each other and not being crystallized in the right place. can 
> i omit them and replace ADP's with MG-ATP? or I should introduce this 
> topology to gromacs?
> regards
> sajad 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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