[gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose

[Mark Abraham]

parichita parichita wrote:
> Thaks for your suggesion... 
>  
> I want to use Gromacs for MD on my disaccharides in explicit water box.Now, the 
> problem I encounter is that the pdb2gmx produces the topologies where hydrogens 
> sitting on carbons are condensed on carbon atoms they sit on. I need them explicitly 
> since I would like to study the NMR coupling contanst of hydroxy protons and C-H protons.I 
> mean 3J(H-O-C-H) and measure the distance between the C-H proton through the glycosidic linkage. 
> So my questions are;
> 
> 1- Are the force fields(45a3,53a5) that are implemented in Gromacs capable of taking care 
> of hydrogens sitting on carbon atoms in a sugar molecule explicitly?

See below, and http://wiki.gromacs.org/index.php/Force_Fields

> 2- How can I most reliably produce topologies for my disaccharide that will 
> be placed in a water box to perform MD?

pdb2gmx... you should find and do some tutorial material to learn about 
this.

> I am quite new to MD methods therefore I apologize already now if I put 
> forward something incoherent.

You should definitely be doing some background reading of textbooks and 
tutorials if you haven't yet come across the phenomena of united-atom 
and all-atom force fields. MD simulations are fabulously easy ways to 
generate very expensive random numbers, and there's no substitute for 
library work and careful experimentation. The first few chapters of the 
GROMACS manual are a good place to start.

Mark