[gmx-users] re: Gromos96 43A1

[Justin A. Lemkul]

Frank Neuhaus wrote:
> Gmx-users,
>  
> I am in the process of deciding on a force field library for a MD 
> simulation. In reading Lemkul et al I get the impression that
> GROMOS96 43A1 is probably the one to use. I am trying to do a simulation 

Hopefully you have not gotten the impression from our work that Gromos96 43A1 is 
somehow a superior force field.  In fact, it is not.  More recent editions of 
the force field probably perform better, and there are other (non-Gromos) force 
fields that may be more suitable for various applications.  Our work was simply 
motivated by the fact that PRODRG produces notoriously unreliable parameters, 
but this fact has been long overlooked in a wide variety of literature and 
Gromos96 parameterization remains somewhat mysterious.  So we made some 
recommendations.

> with a ligase that  binds ADP, 2Mg, D-alanine and D-lactate.  From these
>  authors, I have the impression that PRODRG  is probably not the way to 
> go.  Are there other possibilities? or should I stick to 43A1? Comment

PRODRG is not a good choice for final topologies, but it can be very useful in 
generating a skeleton topology for further refinement.  Alanine and lactate 
should be reasonably easy to parameterize (with alanine being already built in). 
  ADP and ions are already part of 43A1, so the only "unknown" is lactate, but 
given the fact that all its functional groups can be defined by Gromos96 
building blocks, parameterizing it should be no challenge at all.

-Justin

> Thx.
>  
> Frank Neuhaus 
>  
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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